Hmm I just did another flight and this time the warning horn didn't go on. I'm not really sure what I did to avoid this warning this time.

Also the FMS followed my plan nicely this time.

Might it be related to the fact that I alt tab out of the game of press ctrl+enter to minimize or maximize?
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)...