Here goes:

Running a PII System
Voodoo 2 SLI
Orpheus II sound card, WIN98

After spending hours getting this absolute nightmare to work (glide with voodoo2 sli, and sound which i can only get working in DOS mode with Orphinit), I have one more piece of the puzzle before I can fully enjoy this game and that is playing with a gamepad. (love the game but setting it up is a disaster)

So, before I start. My joystick is working fine in windows and in restart in DOS Mode in all other games.
What happens is, when I first run the setup program it says "searching for joystick". It gives no indication of whether it found it/its functional etc
When I go to controller setup, it asks me to hit enter to select a new key or joystick movement or button. At this point it either does nothing, hangs forever, or crashes.
The exact same thing happens in DOS, though a little more stable and usually just does nothing.

If I unplug the joystick, the same thing happens.
Only if I disable the gameport, only then am I able to at least change a key binding.

It's somehow receiving wild information from the gameport and bugging out?