We have a fairly new install of SCOM 2012 R2 and are slowly adding servers. It's going fine for the most part, but CPU utilization alerting doesn't work.
I'm (currently; also tested with 2008 R2) testing on a Windows Server 2012 R2 Full install with one vCPU. I fire up Prime95 and leave it on for an hour, so that CPU is constantly at 100%, but no alert is received.
I created an override for the CPU Percentage Utilization Threshold from the default 95 to 80 and CPU Queue Lenght Threshold from 15 to 1. Nothing happens, alerting works otherwise.