Windows 2000 is not validated on S5000VSA, so some driver may be missing or not working. Which driver are you installing? Did you use a tested USB floppy drive to load the driver? Check http://www.intel.com/support/motherboards/server/S5000VSA/sb/CS-022697.htm.
I highly recommend you to switch to Windows Server 2003.
Bear in mind that you are installing an OS which has not been validated on this board. So there wont be any drivers for W2k.
Here is the list on which OS have been validated:
Try to disable Core Multi Processing in the Bios.
Go to Advanced >> Processor Configuration >> Disable Core Multi Processing
One more thing:
Can you try to install the OS as a non-raid configuration.
Configure SAS/SATA as RAID >> Disable.
All the best,