Done some testing and when you drag a window (on mouse move) the app will freeze, its much more noticeable if you press (and not release) the X of the window.
If you play an MP3 in Windows Media Player It will also stop the animation but not the sound, if you play a video file its again not controlled in the same thread + overlay.

I guess the only way to fully bypass it is by creating your own GUI (i.e Winamp, QuickTime Player), am I wrong?

EDIT: OOPS ops: I does work, I uploaded a Threaded demo to:
www.global-rd.com/ariel/freeze.zip