Is the ProfilerAgent service on the fileserver running? If yes, it sounds like an agent registraion issue. More than likely the Profiler EventReceiver service has bound to non standard port because of a port conflict. Check the Settings --> Profiler Server section, then Server Setup:All, then click on the Server tab and note the SNMP Trap Port. Then edit the core.xml file that you can locate directly under the Agent install directory, and change 162 to match the SNMP Trap Port.
Thanks. That was exactly the problem. I installed the profiler server on my Orion test server box and the snmp trap service was already listening on port 162. After I updated the port on the file servers and restarted the service, they immediately showed up in profiler.