You understand correctly, though from the documents I've read in the past, Windows 2000 Server requires different licensing than Windows 200 Professional.
We installed the Remote Agent on the Windows 2000 Server machine, but have been unable to back it up for what we assumed was a licensing issue. When we go to make a new job, we go to the "Remote Selections" list and expand "Microsoft Windows Network" and our workgroup. From there, we can see all of the machines in the network, including our UNIX/Linux machines running the Remote Agent. All of the machines that can be selected here have white "check boxes" and all of the UNIX machines are gray, as they cannot be checked here. The UNIX machines, of course, can be selected in the "UNIX Agents" section.
The problem is, "Hydra" (Our Windows 2000 Server machine) is also gray, as if it were a UNIX machine. This makes it unselectable in the Microsoft Windows Network area, and it does not show up in the UNIX Agents area.