Here's my 2 cents (pen'orth). I recently upgraded my PC with a new mobo and cpu. I was lazy and just added my system hardrive to the mobo without doing a reinstall. The graphics from my GeForce 2 were OK but there was a jerk in the action every 1 second.
I later decided to do a clean install of Windows 98SE and the problem disappeared. FWIW. HTH
I built a new system this last Christmas, (xp1600, gf2 ti200) and had a similar problem. Everything ran fine, but the framerate just wasn't there. You could see the studdering when you ran around in q3, ut whatever. I wasted my whole Christmas vacation on this ****...trying everything, reinstalled 98se over and over, vid driver, mobo drivers everything..and nothing helped.
Anyway a friend gave me a copy of win xp to load up and try out. Believe it or not this fixed everything. All the games started running oh so smoothly. I still don't know what was wrong with 98, but was more than happy to go with xp.
I'd try borrowing a copy of xp if possible and try loading it up. Don't buy until you know it will fix the problem. It's not a cheap solution, but it was worth it to me to get the damned thing running properly.