UPDATE: I changed the PDF standard to PDF/X-4:2010 and the master page number is now in the right place. I guess I can consider my problem solved, but that was an incredibly frustrating (and potentially VERY costly) glitch. If anyone from Adobe wants to weigh in and help me and other users understand what happened, that would be wonderful.
Have you installed the latest patch for your version of InDesign? For CS5 that's 7.0.4, for CS5.5 it's 7.5.2.
I'll take a guess, Your original PDF export was not embedding the font, which caused the type to wrap. If you make a new layer on your master page and move your page number there, that should fix it for your original export settings, although you really do want to continue to embed your fonts.
Help > About InDesign... shows that I have Version 7.5.2
ID embeds fonts automatically during export as long as they are not restricted. There's no way to turn it off, so if the font is not embedding it is because it is restricted and cannot be embedded without viloating the font license, which ID will not do.
I was hoping this might be one of the bugs that got fixed, but apparently not. An export to .idml and working with that might fix it, might not. See Remove minor corruption by exporting