We were seeing high CPU usage (98-99%) for MonitoringHost.exe on many servers with managed agents in SCOM R2 across a mix of platforms (Windows 2003, 2008, virtual, physical, SQL, 32-bit, 64-bit) which would grind the server to a holt and dramatically affect multiple VMs if the affected server is a Hyper-V host. Our short term fix was to rename the C:\Program Files\System Center Operations Manager 2007\Health Service State directory and restart the ‘System Center Management’ service.
We’ve recently applied this hotfix – http://support.microsoft.com/kb/968967 – which has now permanently fixed the high CPU usage issue. Looks like the underlying cause was MSMXL 6.0 related.
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