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Are there any problems with running the TS licensing service on a Windows 2000 server and connecting to Terminal Services running on a Windows 2003 server in the same domain? It seems at times that the Windows 2003 server cannot find the licensing server. Also, how will the licensing work in this case? I know that the licensing requirements are different for Windows 2000 and Windows 2003.
If you want to use Win2k3 TS licensing, you'll need a W3 licensing server. Check the Event Logs. What error messages are you seeing?