I’m not a big fan of Installing things over and over again, specially not for my LAB with Intune connected and other systems. So there wasn’t a Problem, to Upgrade my System Center Configuration 2012 Manager SP1 Site to R2 Version. But the underlying Server was still a Windows Server 2012 RTM, and not an R2.

This works fine, but I wanted to upgrade my Servers, there were 2, my SQL Server and the Primary Site Server for SCCM 2012, to Windows Server R2. Because I already made some good experiences with In place Upgrades of the Windows Servers (also from 2008 R2 to 2012), I decided to do the same with my SCCM infrastructure. Again: I did this all in my LAB.
But even in my LAB, I was sure to have a Backup of the System to restore them if necessary. First, I upgraded my Server running SQL. This was quite easy, and took about 40 Minutes. SQL was up and running after this, and I could test the Connections from SCCM and everything was fine.
So I did go on, and upgraded the Server which is running the SCCM Primary Site. Also this step was done without any Problems, and SCCM was running afterwards. Until now, I only considered one Problem: I could not use the Remote console anymore, so I checked the SMSAdminUI.log and found an Access Denied error. I checked the DCOM Permissions, but those where fine. Then I checked the WMI Permissions, and those weren’t ok. I needed to add the SMS Admins, and the Remote Console worked afterwards.
Check this blog, to check or resolve WMI Permission Problems: http://anoopcnair.com/2011/10/27/configmgr-sccm-how-to-verify-wmi-permission-for-console-access/

Hope this helps
Martin