I have set one of the programs so that after running "Configuration Manager Restarts Computer". I am familiar with the progress bar that appears when the last 15 minutes is counting down but I noticed this message today. I guess I've never paid attention or does this "Windows Will Shut Down In Ten Minutes" box always appear in the middle of the screen before the computer is restarted automatically?

Hi,

Some blogs said this is a virus. The following blog decribes some steps to remove it. You could check if it helps.

http://blog.teesupport.com/infected-with-you-are-about-to-be-logged-off-virus-remove-you-are-about-to-be-logged-off-virus-manually-step-by-step/

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Both boxes are from Windows are not a concern. the first box "you are about to be logged off" is normally from
windows.  SCCM normally hides these "other" Windows messages but on Windows 8.1 I normally see these when you start to get dangerously close to the restart timer.