As for the glitch, basically all that needs to be done is this: During a match, do your button config. Have the 'main player' (sometimes player one, sometimes player two, which ever the profile is tied to on your PS3) save his config first on Custom 1. Player 2 does Customer 2 - 4, saves it, and goes to character select. Pick your character, play your match, win lose, who cares. Now, go back to character select screen instead of hitting rematch. Have the 'main player' select his character first, BAM, both players are now running Custom 1 or default settings.
The reason behind this is because the game was originally designed for Xbox 360, where both players need a profile to play (hence why when playing on 360, if 2nd player jumps in, it'll ask if he wants to make a profile. If he doesn't, it'll just make him a dummy profile for the game). The dummy profile is still on the PS3 version, but you can't access. And because it's only running on one profile, it just assumes both players are running the same settings.
From what I was told, best ways to avoid this, have controllers running player 2 or 3, or even 4 to 5. Only button config on Character Select... and I think that's basically it. I don't know how reliable this resolves this, but yeah...