A question: was the colony ship filled with population? That would be a tremendous boost if they breathed a different atmosphere. Would need to transfer them to a planet or other ship before you demantled the ship
One other quirk I noticed was during the middle game I had a partnership treaty with an empire who had been on the short end of a war with another AI empire. My score clearly indicated a superior advantage of my partner. I tried an even trade for colony tech and was rejected. The next turn I demanded the tech in tribute and received it?!