Copy all the GWX 3.0 Commander files over into SH3 Commander, EXCEPT for Ship names.cfg.
Also, enabling mods during patrol and without rolling back SH3 commander can and will cause problems. Try starting SH3 and loading your patrol without SH3 Commander, and see if it works then.
Edit: Oh noes! Attack of Langtree's brothel!
I don't even know who the bugger Langtree is
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