Thanks for the reply: in creating a minimal example, I found what was causing the problem. I was using the fullpage package, when instead I should have been doing this:
I am using the memoir class for my thesis. I am supposed to put the page numbers 1/2" down from the top of the page and 1" in from the right side of the page (so upper right hand corner).
Right now I am using this to get the page numbers in the right place: