The installation of this agent is still in progress. If a computer remains in this state for an extended period of time, reject the computer from this view and retry discovery and agent installation.
If you are seeing this kind of issue, chances are you are not alone.
What causes this issue can be as simple as a manual restart of the SCOM 2012 SP1 Agent's service or as complex as manually removing and installing the agent on the Agented Computer.
WHY DOES THIS HAPPEN
If you are used to working with SCOM 2007 -- as I have been from SCOM 2007, SCOM 2007SP1 and SCOM 2007 R2 -- the notion of having to deal with: C:\Program Files\System Center Operations Manager\Agent\Health Service State\Connector Configuration Cache; is all new.
In this directory will be folders for each Management Group using the same agent and after opening that folder you will find a configuration file in XML format.
When he SCOM 2012 SP1 System Center Management service is running on the agented computer, it looks for these configuration files to initialize its settings.
If it doesn't find any, it will rebuild them based on the information in the Operations Manager Agent's
information and only after it has connected.
While running, the Agent does not look at any new configuration files. Nor does it create new configuration files.
The service needs to be stopped, cleared of any folders below C:\Program Files\System Center Operations Manager\Agent\Health Service State\Connector Configuration Cache
and the Operations Manager Agent utility in the Control Panel needs to have the correct information in it before restarting the System Center Management service.
Otherwise, you get: The installation of this agent is still in progress. If a computer remains in this state for an extended period of time, reject the computer from this view and retry discovery and agent installation.
If you think about it, because the Agents are able to provide two way communications, this makes perfectly good sense. If you go to the SCOM 2012 console and try to install an agent on a machine which already has an Agent installed and it is running and communicating to a SCOM 2012 Server, it stands to reason that the installation will be successful.
However, because it is running, the new information is not initialized because the System Center Management service hasn't been restarted.