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Yes you can ..But ... You don't have have to install the AD-Agent on a domain controller! You can install it on any member server.Cisco has a perfect howto: http://www.cisco.com/en/US/docs/security/ibf/setup_guide/ibf10_install.html
'I am using the built-in radius function'Witch built-in radius function are you using? IAS from Windows 2003?In that case you the ports 1812 and 1813 are allready taken by the radius services from IAS.The AD-agent is a small radius server by itself. ...