Only other thing I can think of then is if you installed any mods after running SH3 commander. You have to make sure you do a roll back in commander before adding any mods.
Only time I ever had this happen to me was after a fresh install and adding all mods I realized I had forgotten to patch up to 1.4 first.
Keep at it bud. Im sure someone here will be able to get you straightened out soon.