Yeah, SH3 Commander is primarily focussed on careers, although it does support individual missions. You can overcome your problem by using the "Standard SH3" crew option in SH3Cmdr, which forces SH3Cmdr to use whatever crew config files already exist in SH3 (in other words, ignoring the files included with SH3Cmdr).
Be careful though, that I do not think this will work for RUb users, as RUb uses essentially the same set of career files that SH3Cmdr does (ie the "Realistic" crew). So you may still have this problem, even when not using SH3Cmdr.
If this is the case, then I would use SH3Cmdr's new ability to include your own crew configs and I would create a new crew folder in SH3Cmdr called "Stock SH3" or whatever and copy in the stock SH3 crew_config_xx.cfg files. Check out the help file for more info.
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