This issue still crops up in Operations Manager 2012. However, I experienced a little twist. In Marnix's post, the "NT Authority\System" account was denied. What I noticed was that the account simply wasn't there at all. In the environment, there were two domain controllers, running Windows 2008 R2 64-bit and both showed up gray after installation of the agent.
Logging into the domain controllers, I ran the HSLockdown tool, adding the local system account as follows:
Browse out to the agent folder in \Program Files\System Center Operations Manager\Agent
Run HSLockdown /L to show the account status. Notice in my example that local system is missing.
Run HSLockdown /A "NT AUTHORITY\SYSTEM" to add the local system account.