Depending on which of the four phases of competition
- autonomous-disabled/waiting for start,
- teleop-disabled/waiting for start,
that you're running the joystick settings are not sent to the NXT. For the first three "NULL" (zero) values are sent. Only in the last case are the joystick values sent. If you think about this, it all makes logical sense. The fourth case is the only time that your program should see joystick changes.