At a customerssite this error popped up in the SCOM Console: IIS Discovery Probe Module Failed Execution.
When looking at the error description this information was given: Error initializing IISDiscoveryProbe Error: 0x80090006 Details: Invalid Signature.
When I googled for this errormessage I soon found this KB article from Microsoft. Eventhough it talks about connecting to SQL-server the errormessage is the same.
The server experiencing this error is Windows 2000 Server based and had IE 5.x running. After 'upgrading' it to IE 6.x the errors were gone and all is well again.
The discoveryprobe is running like clockwork now on this server.
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