Well the old “Manually installed agent that doesn’t appear under pending management” situation still exists in SCOM 2012. What is different is that the powershell cmdlet get-agentpendingaction no longer works.

Instead we have the following cmdlet Get-SCOMPendingManagement which provides you all agents
that are in pending management and with Approve-SCOMPendingManagement you can approve the agent you need to.

For a specific agent open the Operations Manager Shell and enter:
Get-SCOMPendingManagement | where {$_.AgentName -eq “ServernameFQDN“} | Approve-SCOMPendingManagement