When I switch to another small window over the Aerofly window, a Notepad window, or GmapHD, for example, AFS2 keeps running, but I lose the ability to move the controls with the joystick.
I have no such problem in FSX or X-Plane.
I am running Aerofly in full-screen mode, I think. Could that be my problem? How do you switch between full-screen and windowed mode? (I couldn't find it in the Wiki or on this Forum).