I have my PDF display set to 'automatically resize', for both normal and full screen views. After I use the full screen view, and then exit to normal view, two kinds of problems occur. First, the page is zoomed out in the normal view; right-clicking the view shows that 'automatically resize' is still checked, however. Second, sometimes Skim refuses to remember which page I was at in the full screen view, and jumps to the title page.
I doubt we can fix this. Displaying and proper display update is the responsibility of Apple's PDFKit. It is clear by now that Apple has gone much too far in drawing optimization in 10.9, as it often fails to update displays properly. It's a big regression that I hope (but doubt) Apple will fix sooner rather than later. My guess is in 10.10.