All I can suggest is that even if the video driver download was exactly the same file for both Win2K and Win98, internally they will probably be doing some things differently, and so what works fine on one OS might not necessarily be perfect on another.
Overheating could cause random crashes. Do you play many other intensive games on the system?
Audio problems can crash machines at odd moments. Trying disabling audio completely if there is a some kind of set-up option or command-line option to do this (I don't have it installed, sorry) and see whether that solves the problem. (Not that you want to remain without sound, but it might narrow the problem down, or eliminate this as a cause if it still crashes).