I have experienced some strange behavior with the Terraformer as well. I haven't checked recently, but when I first built one, I was unable to move it unless I put it in a fleet first (even just a fleet by itself).
I stumbled upon this too. If it is Terraforming it will not want to move to another planet, but you can tell it to move to an open hex near the sun. After that it will accept commands to go anywhere you want.