The position of headers and footers is calculated by placing them halfway between the start of the margin (that is, where the text ends) and the edge of the printable area of the page. The printable area of the page may not always be the same as the edge of the page, which means that headers and footers can sometimes be closer to the text than you might want. The printable area is determined by the printer (PDFs on the Mac are generated by using the print engine, which uses printer settings). So when you see this sort of thing, it’s because your printer is telling Scrivener that it cannot print on quite a large area around the edge of the page, so Scrivener moves the header and footer in.
You can override the printer settings as follows:
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Open up Page Setup. If you have “Use project page settings” ticked in the Page Settings of Compile, then you call up Page Setup by going to File > Page Setup; otherwise click on the button in the “Page Settings” pane of Compile.
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In the Page Setup pane, choose the size of paper you want to use, and make a note of its dimensions (when you select a paper size, its dimensions are shown beneath the paper size pop-up, e.g. “210mm x 297mm” for A4).
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Then, from the paper size chooser, select “Manage Custom Sizes…” from the bottom of the menu.
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Click the “+” button to add a new custom paper size and name it something easy to recognise (e.g. “A4 (No Margin Limits)”).
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In the box that appears, in the “Dimensions” text fields at the top, enter the dimensions you noted down in step (2).
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Then, for “Non-Printable Area”, select “User-Defined” (this is the part that your printer is causing problems with).
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Set each of the non-printable values for top, bottom, left and right to something sensible - a couple of millimetres, or even just set them all to 0.
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Click “OK” to save your custom paper size.
You can then choose this custom paper-size for generating your PDFs. You only need to do this once for each paper size you want to use - once you have set up a custom paper size, it will be available to all projects (and, in fact, across all applications, since this is just a feature of the way Mac apps generate print-outs and PDFs, and it is an OS X feature, not a Scrivener one).
Hope that helps.
All the best,
Keith