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?!