Might it be related to the fact that I alt tab out of the game of press ctrl+enter to minimize or maximize?
I run FSX in windowed mode for the exact reason of having to press CTRL+ENTER to return it to full screen. Doing that never affected any of my flights. I doubt that it will.

Also something that I probably did wrong was to turn my apu off while I was in flight (I forgot about it on the ground)...
All the APU will do when it is on, during a flight, is consume more fuel as well as provide more power (possibly). I use ground power and ground air when parked, so I rarely turn the APU on. I start the engines using ground air.

Mark