Steve -
I am still using 3.1, but I suspect that this bug is the same in both. In a recent battle one of my governments had two jump ships take heavy damage, knocking out each of their jump drives. In the aftermath of the battle they had time to perform damage control/repairs, and one of the jump ships was able to repair its jump drive enabling the squadron to return to the solar system. Or so I thought. I gave the squadron with the repaired jump ship orders to transit out of the system and advanced the time enough that they should have jumped. They did not jump, and the log had the following message: "Squadron cannot carry out its order as at least one ship is larger than the ship with the highest jump rating."
I checked, and none of the ships were larger than the jump ship (they couldn't have been, since the same jump ship conveyed them into the system in the first place). Just to be sure of what was going on, I took all of the ships out of the squadron except the repaired jump ship, and then ordered it to transit again. Once again it did not transit, and the same message was generated, indicating to me that while the jump drive was repaired, somewhere in Aurora it thinks that the ship still has no jump drive. The Individual Unit display shows that the ship has a jump drive, but obviously there is some array somewhere that was zeroed out when the ship received damage, and then not restored when the ship was repaired through damage control.
Kurt