This is not a SH3 Commander problem.
Did you start a new campaign before trying to launch through SH3 Commander? SH3 Commander uses files that SH3 sets up, so if you're starting a new career through Cmdr without having anything set up there are no files for SH3 Commander to read.
Try doing the whole of your first patrol (the practice one, before the war starts) without using SH3 Commander before trying to start with SH3 Commander and it should solve your problems. If not, let us know...
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