Fix Joystick, Fix Joystick, Fix Joystick.

The Analog stick isn't scaled right still.
On the xbox stick, pushing it 1/2 way in a direction makes the n64 game think the stick is all the way in that direction.
If you continue pushing 3/4 to full in a direction, the game can do unpredictable things, such as thinking the stick is back at center, or the stick is being pressed in the opposite direction (wrap-around).
A good game that makes the problem obvious is Buck the bumble bee. OK maybe it's not a good game, but the problem with the stick really shows up in that game, making it nearly unplayable.
Adjusting the sensitivty -100% to 100% doesn't Fix the problem.
Mike
Mike, that's an interesting problem that you are having. It would be best to test using a different controller and/or different controller port to see if you still get the same result. Then post your results here and the dev's will have a better idea of the problem - and what could be causing it.