I believe it’s tied to the Thrustmaster TCA quadrant special logic for handling lift off buttons (Engine start switch, etc…) and for how the internal firmware handle it’s extensions (flaps lever, spoilers lever, etc…)
With the TCA quadrant plugged in, I have a similar issue upon pressing esc and resume with the A320 : the game extends full spoilers and full flaps.
Then unplug the TCA quadrant and… magic no bug !
Then plug it back : bug happens again.
I have found a fix :
I do not have the Quadrant extensions (flaps lever and spoilers), but the game already has these buttons and axis configured. When removing these inputs from the assignments, I no longer have the problem.
The non-existant axis’ are probably applied as their default position (fully deployed).
Maybe you can find a hint for your engine stopping issues (try leaving the engine start or the engine master to on ?)