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If you cannot discover WMI metrics for some applications on Windows hosts, you might need to "resync" the WMI agent on the Windows server:
On Win2000 hosts, run the following from a CMD window:
winmgmt /clearadap # clear all counters
winmgmt /resyncperf <process id>
You have to find the process ID of the winmgmt process in the Process tab of the Windows Task Manager.
On XP/2003 hosts, you need to use:
wmiadap /f
These problems are described more fully in the Microsoft KB article 820847.