Did you know that ctrl-k will disable/enable your joystick in Flight Sim?  I didn't.

I can imagine accidentally hitting that key combo and then having a heck of a time trying to figure out why you can't control the aircraft with your joystick.  There isn't, after all, any visible feedback that your joystick has been disabled.  Is autopilot on?  No. Is my joystick unplugged? No.  etc...