You have to open SH3 at least once without going through Commander in order for Commander to work. Not sure why but I think the game has to create files the first time you load it that Commander needs to access when you run it for the first time.
Anyway I always forget that after a fresh install. I don't think you have to load a mission or start a career, just open the game and let it load one time and then exit. Then open Commander.
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