If you use SH3 Commander, you must install special files for it to use with the GWX3 mod, have you installed them? Also IIRC, there are limitations in the usage of the Commander, not everything goes in the settings. Maybe re-read the behemoth manual about it...
But that's only a possible reason. I guess it should be possible to edit your savegames to start from where you want, I do it in SH5, but I don't know the procedure in SH3.
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