I can confirm that using:

options nvidia_new NVreg_Mobile=1
NVreg_RegistryDwords="PerfLevelSrc=0x2222"

has fixed this problem. I've not found blinks anymore in the last two
days, using the computer 16h+ a day.

** Changed in: nvidia-kernel-common (Ubuntu)
       Status: New => Confirmed

-- 
Occasional screen-wide "blink" when using opengl apps (compiz also) and Nvidia 
cards
https://bugs.launchpad.net/bugs/164589
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