Hmmm... Sounds strangely familiar. I know that I have been in the Windows joystick calibration screen and watched the crosshairs jumping all over the place. Moving the joystick affects the crosshairs, but with the jumping around it's not usable. I don't really remember when or why I had these problems, though, or if it was even with the Dual Strike hack.
I guess this response is fairly useless, except to say that you're not completely alone.