Bumped into an Alert in SCOM 2012 R2 which monitors (among many other things) a SCCM 2012 R2 environment. The Alert ConfigMgr Site Role Issue kept popping up where the Alert itself didn’t give that much information:
Cause
Since the Alert was triggered by a Monitor the Health Explorer gave much more information about the real issue at hand here. As it turned out the ConfigMgr Site Role Issue Monitor is nothing but a rollup Monitor: the real work is done by Unit Monitors and their state changes rollup to the ConfigMgr Site Role Issue Monitor.
The Unit Monitor Notification Server Windows Firewall Block Monitor had a Warning status and the description told me the cause of it: ‘…This monitor indicates whether Windows Firewall on Management Point Name does not allow clients to connect to the Notification Server…’
However, there weren’t any issues at all. The Notification Server could be contacted without any issue by all the clients. So now what?
The FIX
As it turns out from this TechNet Forum question, there is an issue with the way SCCM itself installs the Notification Server and puts that information into the registry.
The registry entry HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\SMS\Operations Management\Components\SMS_NOTIFICATION_SERVER\D07ACE61-FB84-4461-9F52-ABBA07C2EE3A\Severity should be set – after successful installation – to 1.
But somehow this doesn’t happen, instead the registry entry is left at 2, resulting in the earlier mentioned Unit Monitor to change state (Warning), rolling up to the rollup Monitor which fires the general Alert without any real information…
As stated in the same question the ‘fix’ is manually modifying the entry by setting it to 1. I only did this when I knew for certain that the Notification Server is running well and working as expected. Thank fully, every single bit processed by SCCM is logged (and not just once and at one place…. 
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