Might be a glitch, try and accompany them with a warship, see what speed they travel on then. I'll try and check it out as well today
I can confirm. I researched Magdrive and all of my other ships upgraded their engines EXCEPT the colony ship which still has a Nuclear Drive. Even my ships found in ruins, my free support ship, and a militia built cruiser I got from an event all got the Magdrive automatically. Odd that the Colony Ship does not.
There's a bug somewhere. In my case, I researched fusion drive and had all my ships grouped at home, including a colony ship. None of them upgraded, even after I pulled away the colony ship. A series of saves is attached, see if you can replicate the issue
Good catch. There was a bug that was preventing all stationed fleets from updating their drives. In transit fleets drives were being updated ok when they arrived at their destinations. So, say you research Magdrive, your stationed fleets would not update. When you moved a fleet somewhere it would go with the old drive, but when the fleet reached the destination it would automatically update. This is now fixed in the dev build.
Ha, I was not crazy, after all. Well maybe this is not proof of that, but I will go with not crazy for now.