Here is information I pulled from the Shockwave forum by CP_Bomber. Note the Keymapping part. Hope it helps. The key is that you must press "save" in the bottom left after you do a key mapping task (should not be necessary but please do it).
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First off, the Saitek series comes with programming software for a reason - and thats to allow the user to use the stick to its full potential. I would heartily recommend that at some point in time you maybe look into using this software and creating your own profiles. You won't regret it
Secondly, I've just had a look through the key & axis mapping in the game again to refresh my memory before posting here.
Personally, I didn't have any problems.
1) Before you start trying to configure your stick ingame, make sure all switches are OFF.
2) CONTROLLERS, CUSTOM
This is where you can assign the main joystick axis.
Left click on the required axis under the "assign axis" list. The axis should be highlighted red. The move the required axis in it's full range of motion and it should be recognised.
3)If you make a mistake with the axis assignment, highlight the one you want to undo then click on "clear" to return to it's default setting.
4)Repeat until all main axis have been assigned to your liking.
Once complete, click on CONTINUE (top right of screen). And when asked if you want your changes saved, click on YES.
5)IMPORTANT. Now, exit the game back to desktop, then restart it. The game does not permanently keep any changes or settings unless it has been quit & restarted (CTD does not count).
6)Go back to controllers, then click on KEYMAPPING.
7)Scroll through the list, and left click with the mouse once to highlight the current button/key assign to the control of your choice. At the bottom, a message will appear:
"polling input devices.. please press the button you want to map, or the "cancel" button to stop polling. Press "clear" button to remove a mapping."
When you press the required stick button or key, this should be recognised and listed by the function you wanted to remap.
Repeat for all commands required.
8)Now when complete, click on the tick mark of the key mapping window. A box will appear and ask if you want to save your changes. Click YES. Then click CONTINUE, then exit the game to ensure everything is saved.
9)Restart the game, and take a testflight in the instant action missions (like landings) in the aircraft of your choice, and check to see if everything is to your liking. If you need to make any changes, go back to the controllers menu and repeat the above steps.
REMEMBER TO EXIT THE GAME AFTER ANY CHANGES AND THEN RESTART TO ENSURE THAT YOUR CHOICES ARE SAVED.
If when you try to assign a key/button/axis to a command and something else gets assigned immediately, then some input device on your computer is continuously transmitting. Make sure CapsLock & ScrollLock are off on the keyboard when assigning commands.
Go into the game controller section of the windows control panel, check the properties of the joystick and see if any button / switch / rotary is "firing". Memory mode should be on stage "1" and Aux.Mode should be the same. The rotaries should not be giving any signals either. Turn them so they report as "off".
If the mouse if causing the trouble, you may need to check it's double-click speed or try turning off click-lock if engaged.
Also, make sure your drivers & programming software are up-to-date for the sticks too.