Windows Server 2008 R2 RDS CALs can only be installed on and issued from a Windows Server 2008 or Windows Server 2008 R2 Licensing server.
A Windows Server 2008 R2 Licensing server can issue both 2003 TS CALs and 2008 RDS CALs, but a Windows Server 2003 License server cannot supply RDS CALs to Windows Server 2008 or Server 2008 R2 hosts.
If you have an existing Windows Server 2003 TS environment, you can either keep your current Server 2003 licensing server in place to service the Server 2003 environment, or you can migrate your Server 2003 TS CALs to your new Windows Server 2008 R2 Licensing server .
The following two links provide information if you want to migrate Server 2003 TS CALs to a Windows Server 2008 Licensing server:
For more information on how to configure a licensing server, please read the article titled, "How to Configure a Remote Desktop Licensing Server for vSpace 6".