Microsoft just released a new hotfix to deal with ghost agents or agent that are grayed out for an unknown reason. Sometimes it can happen that an agent unexpectedly appear as unavailable without any real reason. We call this ghost agents The workaround was to delete the health service state directory on the computer (root management server, management server, or agent) that is affected. That way the database will be rebuild. But Microsoft has now identified this problem as this issue occurs because...(read more)

Read the complete post at http://scug.be/blogs/scom/archive/2010/05/06/new-kb-for-opsmgr-management-servers-or-assigned-agents-unexpectedly-appear-as-unavailable-in-the-operations-manager-console-in-windows-server-2003-or-windows-server-2008.aspx