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SBS 2008 - BPA finds errors in the console, but not when run manually?


We've installed (and integrated into the console) the SBS Best
Practice Analyser. SBS 2008 Standard.

Our console shows this message for the server:

The Best Practices Analyzer has completed a scan of your system and
has found errors in your system configuration. For detailed
information about the scan errors, manually run the Best Practices
Analyzer tool. Error Count: 1

but whenever we manually run it, we get no errors.

Any ideas? Or where to start looking?