My expierience has been the same as Rockinrobin,I save whenever I need to stop playing REGARDLESS of my game play situation and I have never had a bad save.The game does act a little odd when I first start playing again,usually makes the torp launch sound and shows leaks and such but this all goes away in about 2 seconds and everything is fine.It doesn't actually launch a torp or take any damage but it certainly startled me the first time it happened!
Rockinrobin does this happen to you when you load a save?