I encountered the same problem this morning when MSE scanned only 39 items in 6 seconds. To be safe, I performed a System Restore, using a System Image which I had created on 15th of Sept. After the restore, when I tried to scan using MSE, there was
no change, scan completed in 6 seconds. The only thing left is to uninstall and reinstall MSE. It seems the defect lies in the defination updates from today onwards. I am hopeful Microsoft will look into this soon. Till then custom scans will be the
way to go.
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