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Here's what I submitted to Radar:

Summary: The 'non-printable area' fields (Top, Left, Bottom, Right) in the custom paper sizes dialog are ignored when printing from a Cocoa app. They are correctly used by Carbon apps.

Steps to Reproduce:
[Note: the steps below include specific values, just to be formalist; ANY values will fail, just as these do.]

1: In any Cocoa app (e.g. Safari) choose "Print" (Be sure the full dialog is shown.)
2: Notice that the page preview accurately shows the page size and margins.
3: In the "Paper Size" popup, choose "Manage Custom Sizes..."
4: Create a new Custom Paper Size. Name it "Notepad"
5: Set the Paper Size fields to Width: "5.5 in" Height: "8.5 in"
6: Set the Non-Printable Area popup to "User Defined" 
7: Set the Non-Printable Area fields to Top: "1.0 in", Left: "1.5 in", Right: "1.0 in", Bottom: "1.0 in"
8: Click OK to return to the Print dialog.
9: Confirm that the "Notepad" Paper Size is selected.
10: Note that the page preview accurately shows the Notepad page size, but not the margins.
11: Print the page (as a pdf if you wish to save paper).

Expected Results: A printed page 5.5" x 8.5" with large margins all around and an extra wide margin on the left.

Actual Results: A printed page 5.5" x 8.5" with default margins all around.

Regression: This works fine in all Carbon-based apps.

Notes: I tested this in multiple Carbon and Cocoa applications in both OS X 10.6 & 10.7. The success of Carbon and the failure of Cocoa is consistent across the board.