I take it they aint USB.
I use CH pedals and win98 with a saitek stick. No probs at all.
What the heck are you installing under DOS for?
Do:
1. Ensure you have the correct and latest gameport drivers. (prolly soundcard driver)
2. Ensure Direct X 7.0a is installed
3. Install you JS through
windows with the latest drivers for your stick from CH.
4. calibrate in windows.
5. play
if that dont work try making a custom JS in windows, like a 3 axis with hat and rudders with X buttons. Thats what i did in the end and it works fine.
Spat.