I have a request and a recommendation. First, can you verify the agent is able to log in and take a call? Then, verify that you cannot see the agent on Real Time or Historical reports when you are logged in as webadmin from a known good workstation (everything else works).
If you can see the agent with webadmin user, then you have a partitioning/access class issue.
If you cannot see the agent with webadmin user, the next step I would recommend is a reboot of the CCMA. I have seen lots of unexplainable things on the Web Client/CCMA application that are remedied by a reboot. The Web Client/CCMA product has improved tremendously with release 6, but it still gets confused from time to time.
If the reboot does not work, open a service request with your vendor. You may have stumbled on something in the way your system is configured, patched, or the process you followed that needs attention.