Sorry to bump this topic, but I had been having a similar problem, and I saw a post on this topic in the Help & Training forum which got me thinking about it again.
Here's what I recommend you try:
Go into your main Aces High folder, and open up the folder there called "settings".
In that folder, look for a file which has the name of whatever joystick you use. I use the X-52, and for me the file's called "saitekx52flightcontroller". Move that file to some other folder (you might as well use the desktop so that it's easy to find), and when you have done so, make sure that it is no longer in your settings folder.
Make sure your joystick's plugged in, and start up Aces High. Try looking at your controller settings to make sure that your throttle, RPM,elevator, and aileron controls etc are all mapped correctly, then try and fly a plane.
If this doesn't work, you might want to try reinstalling Aces High, testing it with a mouse, or testing your joystick with another game.
Hope this helps,
Yossarian