1. Avoid unplugging your peripherals.
2. Set your controls/axis assignments as desired. Save. Exit the game. Start the game up again. Verify that your settings are still there. Start up a mission to double-check. If all is well, exit the game.
3. Go to \Falcon BMS 4.33\User\Config and make axismapping.dat[ and joystick.cal read-only files.

That should "protect" your settings from being changed. However, if you want to change your settings, you will need to remove the "read-only" from the above files.