It turns out it was the menu.ini file in traveller mod conflicting with the one in OMEGU 3.
I pseudo merged the OMEGU patch 7 with the traveller mod and it seems to be working correctly. I say "pseudo" merged because I simply merged the two mods leaving out the conflicting traveller menu.ini file.
I figured all I might be missing in that case were some icons in the crew management screen, and for the time being everything else seems to work so I am going with it.
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