I had a similar problem with Win 98. I use the CH Pro-throt and the F16 Fighterstick (both analog).
My solution was:
I pulled the gamecard from my system. I use an SB Live soundcard. (The live cards are powerful enough now to be able to use the gameport on the card)
I set my stick up in windows as a 2 axis, 2 button stick. This allows me to program through speedkeys all of the stick commands for my stick and pro-throt.
Westy is correct too, disable any other soundcard or gameport you are not using on your system. If you do not have a sound blaster Live card, get one or, one which is as efficient.
Good Luck