I hit the Stop Scan button, it asks if I want to stop, I say YES and then duration continues and the Pause and Stop Scan buttons gray out. Any ideas on a fix? Only way to stop it is closing the application.
Can you take a look in the Windows logs to see if cmdagent has crashed when that just happened? The Windows Logs can be found under Control Panel → Administrative Tools → Even Viewer → Windows logs → now look under Applications.