Small bug and work around. Getting the joystick mapping to "stick". It seems it is necessary to create a new copy of the keystrokes file, make your changes to map button x to function y, save it. You then need to exit the game and restart it to get the changes effective. My theory is that the keystrokes file associated with a pilot profile is loaded into memory when the game starts and possibly (haven't tried it yet) when you change pilot profiles and doesn't get reloaded when you maintain the file - so you don't see changes until next time the game starts.

Cheers,
Stonehouse