I had the same problem with my SWPro3D joystick.
I don't use it now because its broken.
What I ended up doing was setting up the joystick in the Gaming Options ( Start / Settings / Control Panel ) as CH Flight Stick or CH Flight Stick Pro ( sorry can't remember which one )
Make sure you check the Rudder/Pedal box.
The only negitive thing with this was that the lower 4 Buttons on the base wouldn't work.
Now some people had success with the lastest driver and with the patch.
http://www.microsoft.com/hardware/sidewinder/downloads/default.asp#3DpatchIt worked for my friend but not for me.
Hope you have better luck with the driver and patch than I did, but my joystick work fine as a CH Flight ...............
Pokie