what do you mean desync? The game runs perfectly fine for me with Peops soft driver and Eternal SPU sound plugin and ePSXe 1.7.0
I think I know what you are talking about now. I forgot FF6 had a multiplayer option. I remember that for the SNES version of the game. Never used it on the PS1 version.
How reliable is your network connection? Are you two in the same room playing from the same connection? Sometimes when me and my roomate played Starcraft online it would randomly kick one of us out every now and then.