Okay this is how I can get it to keep un-checking the VR button.
1) Right I load the sim and put a aircraft on a stand.
2) I load up PF3 and go to options and then hotkeys and make the VR option is active with a tick mark.
3) I then select my flight plan and connect it to the simulator.
4) I start MCE (PF3.ini still shows key active)
5) If I then disconnect PF3 from simulator, leaving the sim running, Now if I leave MCE left running or shut down first, the VR check box becomes "Unticked"
I have tried this serval times and I can repeat it at will, but as soon as MCE has been loaded and running and you disconnect PF3 from the simulator the VR box is "Unticked" when you then check the hotkeys. However when I looked at the PF3.ini I didn't see a change in the active state of hotkey22 it always remained as 0027 and 1, but maybe that doesn't show up unless you do a restart of the PC or something.
Anyway I hope that helps!
Rob