I just wanted to post this here in case anyone else runs into the same problem.
I recently set up a PsychoPy experiment I had been running in Ubuntu on a Windows 7 machine and noticed during testing that I was getting a lot of frame drops. After switching from the default Windows 7 theme (Aero?) to the classic theme, the issue seemed to go away. I went back and forth a few times and confirmed that switching the theme alone was causing up to 20% of critical frames to be dropped.
I'm pretty shocked that the theme could cause such a dip in performance, especially in fullscreen mode. I guess that's just the price you pay for a pretty desktop.