The threshold for the Logical DiskAvg. Disk sec/Transfer performance counter has been exceeded

If you see these alerts generated by your Windows 2008 and Windows 2008 R2 servers with unusually high values, this is due to an issue with the RegQueryValueEx function, which is used in the Average Disk Seconds Per Transfer monitor.

For Windows 2008 R2, apply this hotfix:

For Windows 2008, apply this hotfix:

This is also referenced on Kevin Holman’s hotfix page (a must read for the SCOM administrator).  I’m also referencing here just to help you along in your search results.

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