Do you have other mods installed? Which version of SH3 Commander are you using? Any files or anything that you have changed recently?
Im sure that if it were SH3 Commander doing this, someone would have reported it by now... as thats pretty severe.
Something is conflicting with something else that you have changed recently.
If feasable, I would advise completely uninstalling and reinstalling SH3.
If not, try rolling back SH3 Commander, and launching SH3 itself.
Its not that uncommon that save games are corrupt in SH3, I've had it happen myself from time to time. Usually if I save near a large convoy, that save ends up corrupt.
Provide a few more details, and Im sure someone will have an answer for you.
Cheers.
Jamie
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