Well if its the motherboard then it must be an onboard video and sound card and its having to deal with both at once. Therefore somehow forgets to stop the joystick somehow.

But if its the Joystick then its just a cr*p one, I'd recommend upgrading it to USB if it is the Joystick.

Try another one (joystick that is) that works, maybe borrow it off a friend or something, see if it works, if it does then its your joystick, if it doesn't then its your motherboard and you need to buy a decent video card.

But hey