Hi, haven't used 2000, I jumped from 98se to XP Pro. and I love it! Big improvement. Now I've found my way round the system, it's a joy to use.
Had it running for about five weeks now and not a single problem, (Did a format two days back, for a unrelated reason). Clean install each time, rather than overwrite. Personally I think it's the best way, but many others have done an up-grade with no problems.
Taking in to account the above, I never had any problems with 98se either, so would not recommend an up-grade just to solve problems with your sys. If you do have any conflicts at the moment, then I think you will find they will pass on to the new O/S.
If your sys. is stable and working fine, then why not give it a try, as you say, you already have it. Good luck with the install. J.