This is a know issue: SCOM 2012x Agents become unresponsive on Domain Controllers based on Windows Server 2012 R2. I’ve seen this issue on many occasions on the TechNet forums and on the MVP mailing list this was a top issue.
Finally there is a fix for it! Kevin Holman has written an excellent posting about the cause and how to solve it (installing an optional hotfix). On top of it all, this issue can happen on any Windows Server 2012 R2 OS.
Go here for more information.