"Can't-build-buildings-on-conquest-bug": happened with MOO2Civ and Star Trek mods; Star Trek mod forum has a thread on it, I believe (and it was fixed).
BTW, tried the latest version (as did my MP partner, but not together) and we found that it takes quite a long time before you can build ships that are more powerful and faster than 1 square per turn - which seems especially a handicap for the AI. (I was able to colonize 5 systems in 150 turns, but by that time one civ was eliminated - by barbs, I reckon - and I was at 1,000+ scorewise.) Otherwise it was great fun to see all those well-made barb ships.