Is there a gutter set? This is an additional setting that adds space to the left or right side alternating each page when the document is set for double sided printing. It assumes the document is being bound on one side and provides additional space for this purpose.

Also, the page setup applies to a section. If you have continuous page breaks on your page then the page margins may not be coming from the section you expect.

__________________
Andrew Lockton
Chrysalis Design, Melbourne Australia