I'm not sure if this problem is with Front Mission 3 alone, as I haven't tried more than one save with any other game.
At random times, my save game will get corrupted. Thankfully, I save twice at each point. I can resave over the corrupted save and it will load just fine.
Front Mission 3 allows a regular game save and a battle save and both types have given corruption issues. I haven't tried opening the corrupted save with epsxe, yet, although I'll try it.
JJ