We were troubleshooting an issue for weeks (short monthly maintenance windows) where a SCOM agent was unable to be installed on a few particular servers.
After trying everything from scouring the registry to removing all possible signs on the local server, we were not successful in installing the SCOM agent either from the console or manually on the server. Note that the server was being discovered up until the agent software started deploying.
We kept getting an error stating that the computer was already in the process of being managed. So, we turned to the Management Group as our next potential culprit.
Not really knowing what I was looking for, we backed up the OpsMgr DB.
We discovered a table called AgentPendingAction.
After searching this table row by row using Open Table in SSMS, we found 3 entries with the FQDN of our servers that we could not deploy.
We deleted these rows (1 per server) and then reinstalled the agent.
Success! These entries were somehow hanging around and preventing the agent from being installed.
Hope this helps someone.