I encountered an issue today with an instance that was showing up in OEM 11g though you couldn’t get to the database instance management page as the Agent Connection to Instance was reporting Unavailable. I came up with nothing after a few hours of checking logs, monitoring configuration, restarting agent/oms, etc. Everything was correctly configured and there were no errors to point me in the right direction. So by chance I decided to just try to run the clearstate command via emctl and that fixed the problem. So to make a long story short before you start checking everything in the world you might want to try to run the below first. Until now I was unaware that stopping/starting agent and oms wouldn’t clear the state information of the agent, which wasn’t showing as blocking in the first place.
emctl clearstate agent
emctl upload agent
If it doesn’t work, at least you only wasted a few minutes instead of a few hours like I did today.