Was running a couple of simulations with a Conquest when I noticed that my engines were permanently busted. After a couple of tries I managed to get the situation to repeat pretty consistently.
Basically if maneuvering jets are active when a flameout occurs, the system will get stuck in 'active' mode, leaving one jet constantly on, with the rest of the engines disabled forever.
Got this to occur pretty easily using a Condor and just eating pilums to the ass. Also works with a Falcon-class.