SWBighrn,
Try unplugging your joystick after the game starts up and then plugging it back in. Also while it's unplugged, launch a sortie in the hanger and see if your keyboard zoom key still works.
You might, for some reason,be toggling the zoom and its panned all the way out so it doesn't appear to be doing anything, try the bracket [ ] keys and see if they respond.
If you updated your joystick drivers recently that might be a possible issue
One other thought, make sure you do not have the radio consul up, I've noticed that this can sometimes keep your keyboard commands from working, but not sure why this would effect the joystick input