I’m having trouble numbering my pages when I compile my manuscript as a PDF. I put <$p> in the center box of the footer area in the page settings area, but when I compile the page numbers are underneath the text, 3/4 of the way down on the page. Not below text in the footer area. What am I doing wrong or is this a glitch with the updated edition of Scrivener? 
Have you made extensive changes to your compile settings? If not, you could try applying a “Format As” preset and see if that works better.