I am not sure if this glitch was always present, but it seems that on certain aircraft the autopilot and flaps are "turned off" after some time flying - the autopilot is switched off and cannot be switched on again, and the flaps are reset to their original position (in the cockpit), and will not work (at least in the cockpit). The flaps exceeding warning can still be viewed if you press the buttons that "lower" the flaps, however.