That's why I always double save.
I usually have the game running all day and night (and I mostly run at 1-8x TC. I save the game couple of times a day and use my bout number as the name. When I exit SH3 I always use another save name.
With this method I've never had a corrupted save game.


I'm not sure this will help you, but incase you haven’t tried it..
Good luck