techexp RE: Re: SCOM2007R2: How to force agents to appear under "Agent Requires Update" for patching?
I have experienced same issue some months before. can you please post us the Events appearing in Opsmgr log in any one of the manually installed Agent. Also try manually installing CU5 in one manually installed Agent and let's see the result. you can copy CU5 Agent version from Agentsmanaged folder in management server.