Me and Highness talked about this over ICQ yesterday, trying work around the desyncs.
We switched configurations - located at HKEY_CURRENT_USER\Software\Emulators\Snes9x\1.31 for anyone interested - and this is what we came up with:
Even with Highness's settings, I could not play the movie he made.
Regardless of which settings Highess used, he could play any movie he or I made.
If Highness recorded a movie with my settings, I could play it. This last piece is the most interesting - by using my settings, perhaps Highness could record a movie everyone could watch. I'm hoping he will make a short movie and put it online, and see if everyone can play it. If so we should have a working method and could start to actually plan and make the movie.
EDIT: Here's are two 100-% combos of Shao Kahn for anyone interested.
Use improved version2, WIP timing, uncheck Volume Envelope, check Sync samples:
http://133an.sytes.net/~truncated/MK2-100kombo.smv
(EDIT: It was a zipfile before but it got corrupted during upload. Hopefully this one works.)
You might not think this is a "real" combo, but the fact is that Shao Kahn (or any human player, the computer can cheat-throw) cannot get away, because their blocking animation is longer than the attacking animation. There is no way out. Perhaps it's possible to make him not block by playing more precise.
I've had 1 or 2 random desyncs when playing back this movie.