Are you sure you have the correct folder structure? The structure should be
C\Program Files\Ubisoft\GWX\MODS\Mod1\Data etc
and not
C\Program Files\Ubisoft\GWX\MODS\Mod1\Mod1\Data etc
Also since you did not add them while in port you're tempting fate. My suggestion would be to go to port, disable them, rollback SH3Cmd and then enable them. That should work.
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