Started a new game with 1.01 as the Alterians.
When I researched the first sensor improvement, the ship designs went through the usual automatic upgrades.
When I went to build my next ship, my options were:
prototype scout - m3
scout - m3
constructor - m3
constructor - m5
Yes, two types of constructor and no colonizer. However, the constructor - m3 was really the correct colonizer, the name was just wrong. It was "deep root" instead of "light spreader".
I immediately saved, quit, then reloaded and the problem fixed itself, so it must be something with the in-memory list driving the shipyard's display. I have not seen this behavior before, so possibly new with 1.01.