I have played this game since it's release and added hundreds of mods in that time but have never had that problem, this is a weird one!
All I could suggest is since it happens with stock is to check the following:
Using version 1.4b
reinstall SH3
Cripes thats all I
can suggest,
it is obviously an ingame problem so not much point checking drivers etc, if you do find problem please post, I'm interested in knowing.
Good Luck!
Edit: Sheesh, we all posted at the same time!!