This was a well documented issue with Soul Calibur III, unfortunately. I believe it was something that was initiated by moving or deleting some data on your memory card or something like that. Luckily for you, it seems you're not one of the people who's whole card got deleted. I'm really not sure what measures are to be taken to prevent this, but I haven't had it happen yet. I think mainly you just can't mess with anything on the memory card. Don't take my word for it though, I found an FAQ for the issue on GameFAQs, I'd give it a lookover.
http://db.gamefaqs.com/console/ps2/f...corruption.txt