Hmmm... That doesn't sound good. I'm running that board with Win2k right now. However, I am only using one drive on the RAID controller.
What version of the Promise drivers are you using? I downloaded the latest ones from MSI's website (I think they're 1.30b60). Other than a weird problem with the previous version of SiSoft Sandra and single-drive RAID arrays, I think those drivers work OK for the most part.
If you have the capability, I would wipe the install and start over. First flash the BIOS to 2.5 or higher (I'm still running 2.5 because of my "if it ain't broke don't fix it" mentality). Check the Promise BIOS to make sure the RAID array is functional. Then re-install Win2k after re-partitioning and re-formatting (always use NTFS).
Of course, make sure you use the correct Promise drivers upon Win2k setup booting (hit F6, I think). There were two choices when I installed Win2k, and the correct one was not obvious. One is correct, the other is not. I don't remember which one is correct. Sorry.
Also, if I'm not helping any, you might try posting to the forums over at
AMDMB.COM under the MSI topic. There are a bunch of K7T Turbo-R people over there.