There is a known issue where SCOM 2012 agents stop responding on Windows 2012 R2 Domain Controllers but can affect other Windows 2012 R2 servers as well . Kevin Holman has posted an article with the resolution to this issue: Here

“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″