There are a variety of different reasons which can cause an agent to appear as “Not Monitored”. We were debugging some of these on a client site, and ran through potential issues such as these:

We had been debugging the “Not Monitored” agent status from the Administration pane. Once we went to the Monitoring pane and the computers view it became readily apparent why they were “Not Monitored”. These agents were the result of a cloned image which had been put into Maintenance Mode. Once we removed these from Maintenance Mode they reported in correctly.

Summary: Remember, servers which are in Maintenance Mode will appear as “Not Monitored” in the Administration pane. To find these, check them in the Monitoring pane to see if they are in Maintenance Mode.