I’m currently running Beta 7 with media player 0.9.2 and I’m having the same problem. Some movies seem fine and then others go way out of sync. We just watched the movie “Paul” (about the alien) and it went out of sync probably a half dozen times. On one of the occurences, it went out of sync over a period of only a few seconds and quickly got to a point where it felt like we were watching one movie and listening to another. Going back to the DVD menu and then resuming the movie seems to get things back in sync again.
Additionally, this has also happened on some .avi files as well.