Not sure if this is the place to ask this:
I recently installed strike commander and having a hard time getting my Thrustmaster to work with it.
Anyway I tried a lot to fix it and in one of my web searches came across this.
I was having same problem joystick could move in the menus and even use fire to select items but was totally non responsive in the game.
The reason I finally found out is that you have to go into options and choose Flight, and then set you flight control to be the joystick instead of the mouse.
Make sure you save the settings then you should be able to fly your missions using the joystick.
How can i get someone to post the above fix to the wiki page?