Not sure if I have reported this in the past, anyway I'd like to report it since it still seems to exist in the current version.
Reset by movie can provide a different result between the recording and playback. *1 While recording a movie, a reset is done when the player clicks "Reset" from menu. (i.e. outside of S9xMainLoop) On the other hand, while playing a movie, a reset is done when the movie is read. (i.e. inside of S9xMainLoop, probably) Those timing difference can cause movie desync.
I wrote a patch for this before, but I'm not sure if there is a better way to fix the problem. *2 I show the old diff as a reference, then I'd like to help you to know and think about the problem.
http://code.google.com/p/snes9x-rr/source/detail?r=164
*1 Chrono Trigger TAS couldn't be recorded well because of this glitch.
*2 I don't want to write the patch by myself, because it needs to update the platform-independent code.