UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

(Amendment No. 6)

Under the Securities Exchange Act of 1934

NCI Building Systems, Inc.

(Name of Issuer)

Common Stock, par value $0.01 per share

(Title of Class of Securities)

628852204

(CUSIP Number)

Clayton, Dubilier & Rice Fund VIII, L.P.

c/o Clayton, Dubilier & Rice, LLC

Attention: Theresa A. Gore

375 Park Ave, New York NY 10152

(212) 407-5227

Copy to:

Steven J. Slutzky

Debevoise & Plimpton LLP

919 Third Avenue

New York, New York 10022

(212) 909 6000

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

December 15, 2011

(Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition which is the subject of this Schedule 13D, and is filing this schedule because of Sections 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box.  ¨

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Section 240.13d-7 for other parties to whom copies are to be sent.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

On February 19, 2010, at a meeting duly called by the Issuer, the shareholders of the Issuer approved a reverse stock split of the Common Stock (the “Reverse Stock Split”). On the same date, the Board of Directors of the Issuer (the “Board”) approved a ratio for the Reverse Stock Split of 1-for-5. The Reverse Stock Split became effective on March 5, 2010.

Preferred Shares. 249,651 Preferred Shares were issued to Fund VIII in a private offering (the “Investment”) pursuant to an Investment Agreement, dated August 14, 2009, as amended (the “Investment Agreement”), which closed on October 20, 2009. Effective January 4, 2010, Fund VIII transferred 282 shares of Preferred Stock, equivalent to 44,243 shares of Common Stock on an as-converted basis and after giving effect to the Reverse Stock Split, to CD&R Friends & Family Fund VIII, L.P. (“F&F Fund VIII”). 6,346.1178 shares of Preferred Stock convertible into 995,626 shares of Common Stock have accrued to Fund VIII as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations, Preferences and Rights of the Preferred Stock (the “Certificate of Designations”) for the period from December 30, 2009 to March 15, 2010. 7,951.9087 shares of Preferred Stock convertible into 1,247,554 shares of Common Stock that represent (i) the dividend accrual to Fund VIII as a holder of Preferred Stock pursuant to the Certificate of Designations for the period from March 16, 2010 to June 15, 2010 and (ii) a 3% increase in the dividend rate for the period from March 15, 2010 to March 17, 2010 (date on which the dividend for the period ending March 15, 2010 was paid) have accrued to Fund VIII pursuant to the Certificate of Designations. 8,149.4437 shares of Preferred Stock convertible into 1,278,545 shares of Common Stock have accrued to Fund VIII as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from June 16, 2010 to September 15, 2010. For the periods between (i) September 16, 2010 to December 15, 2010 and (ii) December 16, 2010 to March 15, 2011, the Company paid the dividends in cash. 8,395.9366 shares of Preferred Stock convertible into 1,317,216.28 shares of Common Stock have accrued to Fund VIII as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designation for the period from March 16, 2011 to June 15, 2011. 5,766.5894 shares of Preferred Stock convertible into 904,705 shares of Common Stock have accrued to Fund VIII as dividends payable to holders of Preferred Stock for the period from June 16, 2011 to September 15, 2011 pursuant to the Certificate of Designation as modified by a Mutual Waiver and Consent entered into by Fund VIII, F&F Fund VIII and the Company, dated as of September 6, 2011 (the “September 2011 Mutual Waiver and Consent”), which provides, among other things, for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from June 16, 2011 to September 15, 2011. 5,818.9249 shares of Preferred Stock convertible into 912,916 shares of Common Stock have accrued to Fund VIII as dividends payable to holders of Preferred Stock for the period from September 16, 2011 to December 15, 2011 pursuant to the Certificate of Designation as modified by a Mutual Waiver and Consent entered into by Fund VIII, F&F Fund VIII and the Company (the “December 2011 Mutual Waiver and Consent”), which provides, among other things, for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from September 16, 2011 to December 15, 2011.

Fund VIII Cash Dividend. $5,766,548.54 has accrued to Fund VIII as cash dividends payable to Fund VIII pursuant to the Certificate of Designations for the Cash Dividend Period. Pursuant to the Certificate of Designations, until such Fund VIII Cash Dividend is paid in cash, such dividend will be convertible into 904,699 shares of Common Stock. The Company has not yet paid the Fund VIII Cash Dividend.

Preferred Shares. 349 Preferred Shares were issued to F&F Fund VIII pursuant to the Investment Agreement. Effective January 4, 2010, Fund VIII transferred 282 shares of Preferred Stock, equivalent to 44,243 shares of Common Stock on an as-converted basis and after giving effect to the Reverse Stock Split, to F&F Fund VIII. 15.46377 shares of Preferred Stock convertible into 2,426 shares of Common Stock have accrued to F&F Fund VIII as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from December 30, 2009 to March 15, 2010. 19.9051 shares of Preferred Stock convertible into 3,123 shares of Common Stock that represent (i) the dividend accrual to F&F Fund VIII as a holder of Preferred Stock pursuant to the Certificate of Designations for the period from March 15, 2010 to June 15, 2010 and (ii) a 3% increase in the dividend rate for the period from March 15, 2010 to March 17, 2010 (date on which the dividend for the period ending March 15, 2010 was paid) have accrued to F&F Fund VIII pursuant to the Certificate of Designations. 20.4001 shares of Preferred Stock convertible into 3,201 shares of Common Stock have accrued to F&F Fund VIII as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from June 16, 2010 to September 15, 2010. For the periods between (i) September 16, 2010 to December 15, 2010 and (ii) December 16, 2010 to March 15, 2011, the Company paid the dividends in cash. 21.0165 shares of Preferred Stock convertible into 3,297 shares of Common Stock have accrued to F&F Fund VIII as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from March 16, 2011 to June 16, 2011. 14.4348 shares of Preferred Stock convertible into 2,265 shares of Common Stock have accrued to F&F Fund VIII as dividends payable to holders of Preferred Stock for the period from June 16, 2011 to September 15, 2011 pursuant to the Certificate of Designation as modified by the September 2011 Mutual Waiver and Consent, which provides, among other things, for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from June 16, 2011 to September 15, 2011. 15.5664 shares of Preferred Stock convertible into 2,285 shares of Common Stock have accrued to F&F Fund VIII as dividends payable to holders of Preferred Stock for the period from September 16, 2011 to December 15, 2011 pursuant to the Certificate of Designation as modified by the December 2011 Mutual Waiver and Consent, which provides, among other things, for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from September 16, 2011 to December 15, 2011.

F&F Fund VIII Cash Dividend. $8,061.46 has accrued to F&F Fund VIII as cash dividends payable to F&F Fund VIII pursuant to the Certificate of Designations for the Cash Dividend Period. Pursuant to the Certificate of Designations, until such F&F Fund VIII Cash Dividend is paid in cash, such dividend will be convertible into 1,264 shares of Common Stock. The Company has not yet paid the F&F Fund VIII Cash Dividend.

Preferred Shares. 250,000 Preferred Shares were issued to the CD&R Funds pursuant to the Investment Agreement. 6,361.58152 shares of Preferred Stock convertible into 998,052 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from December 30, 2009 to March 15, 2010. 7,971.8138 shares of Preferred Stock convertible into 1,250,677 shares of Common Stock that represent (i) the dividend accrual to the CD&R Funds as holders of Preferred Stock pursuant to the Certificate of Designations for the period from March 16, 2010 to June 15, 2010, and (ii) a 3% increase in the dividend rate for the period from March 15, 2010 to March 17, 2010 (date on which the dividend for the period ending March 15, 2010 was paid) have accrued to the CD&R Funds pursuant to the Certificate of Designations. 8,169.8438 shares of Preferred Stock convertible into 1,281,746 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from June 16, 2010 to September 15, 2010. For the periods between (i) September 16, 2010 to December 15, 2010 and (ii) December 16, 2010 to March 15, 2011, the Company paid the dividends in cash. 8416.9531 shares of Preferred Stock convertible into 1,320,514 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from March 16, 2011 to June 16, 2011. 5,781.0242 shares of Preferred Stock convertible into 906,970 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock for the period from June 16, 2011 to September 15, 2011 pursuant to the Certificate of Designation as modified by the September 2011 Mutual Waiver and Consent, which provides, among other things for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from June 16, 2011 to September 15, 2011. 5,833.4913 shares of Preferred Stock convertible into 915,201 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock for the period from September 16, 2011 to December 15, 2011 pursuant to the Certificate of Designation as modified by the December 2011 Mutual Waiver and Consent, which provides, among other things for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from September 16, 2011 to December 15, 2011.

Total Cash Dividend. $5,774,610 has accrued to the CD&R Funds as cash dividends payable to the CD&R Funds pursuant to the Certificate of Designations for the Cash Dividend Period. Pursuant to the Certificate of Designations, until such Total Cash Dividend is paid in cash, such dividend will be convertible into 905,963 shares of Common Stock. The Company has not yet paid the Total Cash Dividend.

Preferred Shares. 250,000 Preferred Shares were issued to the CD&R Funds pursuant to the Investment Agreement. 6,361.58152 shares of Preferred Stock convertible into 998,052 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from December 30, 2009 to March 15, 2010. 7,971.8138 shares of Preferred Stock convertible into 1,250,677 shares of Common Stock that represent (i) the dividend accrual to the CD&R Funds as holders of Preferred Stock pursuant to the Certificate of Designations for the period from March 16, 2010 to June 15, 2010 and (ii) a 3% increase in the dividend rate for the period from March 15, 2010 to March 17, 2010 (date on which the dividend for the period ending March 15, 2010 was paid) have accrued to the CD&R Funds pursuant to the Certificate of Designations. 8,169.8438 shares of Preferred Stock convertible into 1,281,746 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from June 16, 2010 to September 15, 2010. For the periods between (i) September 16, 2010 to December 15, 2010 and (ii) December 16, 2010 to March 15, 2011, the Company paid the dividends in cash. 8416.9531 shares of Preferred Stock convertible into 1,320,514 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from March 16, 2011 to June 16, 2011. 5,781.0242 shares of Preferred Stock convertible into 906,970 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock for the period from June 16, 2011 to September 15, 2011 pursuant to the Certificate of Designation as modified by the September 2011 Mutual Waiver and Consent, which provides, among other things for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from June 16, 2011 to September 15, 2011. 5,833.4913 shares of Preferred Stock convertible into 915,201 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock for the period from September 16, 2011 to December 15, 2011 pursuant to the Certificate of Designation as modified by the December 2011 Mutual Waiver and Consent, which provides, among other things for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from September 16, 2011 to December 15, 2011.

Total Cash Dividend. $5,774,610 has accrued to the CD&R Funds as cash dividends payable to the CD&R Funds pursuant to the Certificate of Designations for the Cash Dividend Period. Pursuant to the Certificate of Designations, until such Total Cash Dividend is paid in cash, such dividend will be convertible into 905,963 shares of Common Stock. The Company has not yet paid the Total Cash Dividend.

Preferred Shares. 250,000 Preferred Shares were issued to the CD&R Funds pursuant to the Investment Agreement. 6,361.58152 shares of Preferred Stock convertible into 998,052 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from December 30, 2009 to March 15, 2010. 7,971.8138 shares of Preferred Stock convertible into 1,250,677 shares of Common Stock that represent (i) the dividend accrual to the CD&R Funds as holders of Preferred Stock pursuant to the Certificate of Designations for the period from March 16, 2010 to June 15, 2010 and (ii) a 3% increase in the dividend rate for the period from March 15, 2010 to March 17, 2010 (date on which the dividend for the period ending March 15, 2010 was paid) have accrued to the CD&R Funds pursuant to the Certificate of Designations. 8,169.8438 shares of Preferred Stock convertible into 1,281,746 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from June 16, 2010 to September 15, 2010. For the periods between (i) September 16, 2010 to December 15, 2010 and (ii) December 16, 2010 to March 15, 2011, the Company paid the dividends in cash. 8416.9531 shares of Preferred Stock convertible into 1,320,514 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock pursuant to the Certificate of Designations for the period from March 16, 2011 to June 16, 2011. 5,781.0242 shares of Preferred Stock convertible into 906,970 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock for the period from June 16, 2011 to September 15, 2011 pursuant to the Certificate of Designation as modified by the September 2011 Mutual Waiver and Consent, which provides, among other things for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from June 16, 2011 to September 15, 2011. 5,833.4913 shares of Preferred Stock convertible into 915,201 shares of Common Stock have accrued to the CD&R Funds as dividends payable to holders of Preferred Stock for the period from September 16, 2011 to December 15, 2011 pursuant to the Certificate of Designation as modified by the December 2011 Mutual Waiver and Consent, which provides, among other things for the consent of Fund VIII and F&F Fund VIII to the payment of the dividend in shares of Preferred Stock at the rate of 8% per annum rather than 12% per annum solely for the period from September 16, 2011 to December 15, 2011.

Total Cash Dividend. $5,774,610 has accrued to the CD&R Funds as cash dividends payable to the CD&R Funds pursuant to the Certificate of Designations for the Cash Dividend Period. Pursuant to the Certificate of Designations, until such Total Cash Dividend is paid in cash, such dividend will be convertible into 905,963 shares of Common Stock. The Company has not yet paid the Total Cash Dividend.

Item 3. Source and Amount of Funds or Other Consideration.

Item 3 is hereby amended and supplemented by adding the following:

“In accordance with the terms of the Certificate of Designations, since the date of issuance of the Preferred Stock, the Preferred Shares have accrued the following dividends:

Total Cash Dividend. $5,774,610 has accrued to the CD&R Funds as cash dividends payable to the CD&R Funds for the Cash Dividend Period. Until such Total Cash Dividend is paid in cash, such dividend will be convertible into 905,963 shares of Common Stock.”

Item 5. Interest in the Securities of the Issuer

(a)

Items 5(a)(i) and (ii) are hereby amended in their entirety to read as follows:

“(i) Fund VIII is the beneficial owner of 46,684,103 shares of Common Stock, which it has the right to vote with holders of Common Stock on an as-converted basis pursuant to the Certificate of Designations, without taking into account any limitations on convertibility due to the number of authorized shares available for issuance that may then be applicable. At the initial conversion price of $1.2748 (or $6.3740 after giving effect to the Reverse Stock Split), Fund VIII’s voting interest is approximately 70.0% of the voting power of the Company.

(ii) F&F Fund VIII is the beneficial owner of 116,854 shares of Common Stock, which it has the right to vote with holders of Common Stock on an as-converted basis pursuant to the Certificate of Designations, without taking into account any limitations on convertibility due to the number of authorized shares available for issuance that may then be applicable. At the initial conversion price of $1.2748 (or $6.3740 after giving effect to the Reverse Stock Split), F&F Fund VIII’s voting interest is approximately 0.2% of the voting power of the Company.”

Item 7. Material to be filed as exhibits.

Item 7 is hereby amended and supplemented by adding the following:

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Date December 16, 2011

Exhibit 1

Joint Filing Agreement

Pursuant to Rule 13d-1(k)(1) promulgated under the Securities Exchange Act of 1934, as amended, the undersigned agree that the Statement on Schedule 13D/A to which this exhibit is attached is filed on behalf of each of them in the capacities set forth below.

Dated: December 16, 2011