Then unfortunately you may have borked up your SH3 install. SH3 Commander is an incredibly powerful tool and it makes changes to a number of the files in SH3.
Try loading an older save game as SH3 Commander may not like the last save game.
If that doesn't work try uninstalling SH3 Commander then loading a completely new game without Commander. If the new game works then SH3 is probably not messed up and it may again be a Commander issue.
If these don't work then you may need to reinstall SH3 from scratch. I speak from bitter experience as the same thing happened to me as I didn't have automatic rollback enabled (ALWAYS enable automatic rollback!) and a combination of mods crashed SH3. SH3 Commander only remembers the last set of changes you make, so by restarting SH3 through Commander without rolling it back I made permanent changes to my game. Since then I've used MultiSH3 to keep copies of vanilla 1.4b and unmodded GWX on my system to same me some heartache!
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