This happened to me twice.. and I dont know why. But I wanted to complete my monster book info and decided to hunt the monsters to fill out the .. after getting them all up to the current level... the game crashes and removes all the monsters I just filled up.. I also get an option to load from a backup save -_-. It even removed the two bosses I just beat after and now I cant fight those bosses again till new game... kinda of annoying.
Hmm that's weird. I've finished the game using the JP Windows Vista DVD, as well as the Steam release, and haven't encountered this problem. Assuming you are using the Steam release, have you sent a support request to XSeed so they can troubleshoot it?
Its not the steam version, this is the original pre Windows 7 version. I never had this when I played it without the English patch a couple of years back. Seems the English patch has random shutdowns for everyone that has played it... something to do with the resolution.