Advanced Settings (about:config) for header & footer margins (top, bottom, left, right, unwriteable twips) are ignored when printing to PDF (i.e. Microsoft Print to Fax, and Kofax Power PDF). Works fine when printing to physical printers (paper) (i.e. HP Officejet 9025e).
I can do a workaround for this problem when dealing with left & right margins by adding spaces to commands (i.e. "________&PT" or "&D________").
However, I have found no setting that will lower headers or raise footers off the very top and bottom edges of the page.
I have tried every margin and twips setting I can find.
See photo sample of PDF document where workaround settings (adding spaces) has moved. Text away from left & right edges of PDF document. Also, image showing Advanced Settings is shown.