Today, I ran into an issue when trying to install the SCOM 2012 R2 agent on a domain controller running Windows Server 2012 R2. I found the following technet article which proved useful as it had the error and error code I was getting, but the remediation steps didn't solve my problem.
Troubleshooting Issues When You Use the Discovery Wizard to Install an Agent
Upon further investigation, I could not access the SYSVOL and NETLOGON shares on that specific domain controller from the SCOM management servers running Windows Server 2012 R2.
I remember seeing this sort of issue when accessing shares on a NetApp that we have from a Windows 2012 Server. So disabling the secure negotiate on the Windows 2012 Server solved that issue. So I did the same on the SCOM Management Servers which ended up fixing this issue using the following powershell command.
Set-ItemProperty -Path "HKLM:\SYSTEM\CurrentControlSet\Services\LanmanWorkstation\Parameters" RequireSecureNegotiate -Value 0 -Force
http://support.microsoft.com/kb/2686098
You should also read this which explains Secure Negotiate which is new for SMB3.
http://blogs.msdn.com/b/openspecification/archive/2012/06/28/smb3-secure-dialect-negotiation.aspx