Okay, well I just went through and checked every monster group in the FFI forum and made certain there were no invisible monsters (I think there were around five total). I've uploaded the edit, so just download it, transfer over you old save file, and give it a try.
Also, what level are you right now? I'm thinking the monsters you had trouble fighting were the invisible ones I got rid of (they have roughly three times the defense, two times the attack, and no attack animation, which would explain taking damage for apparently no reason), but if you keep having trouble let me know.
