I have run 3dGS on win2kpro since I purchased (starting with a6.11) it with no problems. I have made no other special efforts/additions to the operating system other than the windows updates and have not installed the accessibility kit.
3dGS updates have run fine in all product update versions. This machine with win2kpro is my primary development machine. I have another (AMD64) with winxp pro and have more problems with 3dGS on it.
As for the difference in compile times it might just be that win2k's virtual memory is not optimised, given that win2k can read above 512meg RAM. Try freeing up some HD space and check your virtual memory settings. Most times it is best to allow windows to manage itself, but this is not always the best scenerio.
Hope that helps.