[Urendi Maleldil]

That custom universal colony module might be your problem. Try adding a separate tech area for it in the TechAreas.txt data file and see if that fixes your problem.

When the game selects starting colony techs I believe it simply selects the first TechAreas.txt entry that will yield a component with the home planet type colonization ability. You might also try moving the component entry around in Components.txt to see if that does anything.

The Colony Tech Mod 2 works by exploiting this behavior, so you might want to download it and take a look at the data files to get an idea of how it all works.