I think it's because you're also trying to use the maneuvering jets. There is an issue with using jets just as engines start to come back online which causes the engines to flameout again. Personally, I'd call it a feature, don't push your engines right into the red just after fixing them. "You just managed to start walking again? Great! Now do the 100m sprint". Though I thought the bug appeared because it was the activation of several more engines (as the Eagle, Falcon and Conquest do have special engines only active during maneuvers or while at cruise speed).