Not sure, Steve will correct me if I am wrong, but I think when the jump drive gets damaged/destroyed, that box gets unchecked to show that the ship is not jump capable. Maybe if the repair function turned it back on too.
It's also so you can turn off jump engines manually in order to force a particular ship to be the jump ship during a combat transit
I've added the re-activation of the jump drive as part of the repair process for v3.11
Steve
