Interesting, indeed! I'm glad you've uncovered what's been causing all these issues. In light of that, you might want to consider disabling the "Pause on task switch" option in the FSX general settings. Even though ALT-TABbing in and out of FSX remains an exercise in frustration regardless, it might help preventing those wonky FMC errors from occuring.

BTW you should Alt-Enter out of FSX not Alt-Tab, Alt-Tabbing can lead to odd things happening (black screens etc).