Well, I have a strange problem.
A little bit of this crazy run using "Smash TV (U).smc".
I'm using SNES9x 1.43 v7 improvement by Nitsuja. The end of this file is supposed to have player 1 pick up a yellow shield, run it into the slow guy who borders rooms, and then the shield piece will fly into a large group of enemies on the right side of the screen. Unfortunately, the shield isn't always appearing, causing a desync.
Playing the file normally causes some missed shots to happen in the second room, and play to just get lazy. Playing again, and fast-forwarding (with the tab button) until the beginning of the second room, the file syncs up more - the enemies are in the right places, and the shield appears (although I still haven't gotten it to play exactly as I did when I recorded it). I'm sure I didn't load bad savestates or anything like that (I don't think that matters with this game anyway). I wanted to work on this run in spare time, perhaps to take small breaks from Super Metroid, but these desyncs have got me holding off. Maybe this is just a game that has desync issues, like Mortal Kombat? I hope not.
Anyway, if anyone has any ideas, that would be cool.