This is not a new system based on a X79motherboard is it?
If so, you need to update the BIOS. To my knowledge, both Asus and Gigabyte X79 mothebards suffered from something very like this until BIOS releases early this month.
Certainly if you want help beyond my purely speculative shot, you need to tell us a great deal more about your system.
The system is a dual Xeon x5680, overcloced to 4.5Gzh, with 48 GB ram. I'm running on a EVGA SR-2 motherboard running the latest bios (as of 2 months ago). Runs like a beast in everything, just this annoying problem that keeps surfacing all the time.
Thanks for the reply!
Best guess is some background process stealing focus.
If it happens at regularly timed intervals of user input inactivity,
I would suspect a power option trying to spin down a drive
or blank the display.
I would start 'GodMode' and check all of the power options.
Create a new folder, and give it this exact name:
Do you have an automatic defrag program like PerfectDisk of Diskeeper?