Speaking (I mean, typing) of joysticks, I'm facing a similar problem too.
When calibrating my Thrustmaster Top Gun Platinum or my Logitech Wingman Extreme Digital 3D for WC3 or WC4 in Windows98 Dos mode,
the joystick signals seems to be fluctuating all the time and when playing the cursor tends to drift.
Anyone can enlighten me a bit about this matter?