i've noticed this too...although it hasnt really caused any performance issues. i probably wouldn't have noticed it at all, but when playing world class bolwing with my 3 year old, he tried using the joystick and the ball went shooting down the lane really fast. i havent really tried to fix it, i dont know anything about your config, but i use MALA with the plugin to automatically load maps when you launch a game, on mine, i'm assuming it is loading an analog map, which is why the trackball games pick up on the joystick input.. so perhaps loading a different map for those games may fix the problem.
of course, if you arent doing it that way, i dont know what may do it.