Hahaha! In my efforts to fix troop design, I was toying with AI tag reqs for the "cockpits," to try to get just one per troop. I copy/replaced the abilities back to the CQ and LS ones after I learned what the actual problem was. I seem to have forgotten to record the AI tags used to make the AI design colony ships, and reused them in the troop testing.
As an interim solution, here is a file that will restore the AI's ability to make all colony ship designs:
Components.zip. Note that this will break muliplayer savegame compatibility.