This is an issue I have been tracking for some time. When you deploy SCOM 2012 Agents on Windows Server 2012 R2 Domain Controllers, it is possible for the agents to stop responding and or sending heartbeats. The agent services will still be running. You will see the events in the OpsMgr event log stop processing, and you might see heartbeat failures as well. I have personally seen this on both of my Windows 2012 R2 domain controllers, which also run DNS and DHCP, and have the AD, DNS, and DHCP management packs imported.
This is caused by an issue in the Server OS (Windows Server 2012 R2), which is outlined at http://support.microsoft.com/kb/2923126
There is a hotfix, which addresses the issue, which is included in the Feb 2014 update rollup hotfix: http://support.microsoft.com/kb/2919394
I recommend you consider deploying this update if you are deploying DC’s on Windows Server 2012 R2. This issue could potentially affect any server running Windows Server 2012 R2 operating system, I have just experienced it on DC’s thus far.
If you use Windows Update – this hotfix is listed as “Optional”: