We had one of our offices roll back from R5.0.12 on Windows 2003. They had issues with the Domino server crashing. After they rolled back, they upgraded Domino to R6.0.3 on Windows 2003 and haven't had any issues. My own Domino R6.0.3 Servers are running on Windows 2000 without any problems. Hope this helps.
Rgds,
John