My Late 2013 Mac Pro 6 Core w/D500 GC's flashes to black twice every 5 minutes or so.
One monitor is Thunderbolt and the other is Display port.
both of them do this at the same time.
Mac Pro, OS X El Capitan (10.11.4)
Some 2013 Mac Pros have a hardware problem
mac pro late 2013 freezes with spinning wheel
http://9to5mac.com/2016/02/06/apple-mac-pro-repair-program-graphics-video/
There is a legitimate blink that occurs when a display is added or removed.
If yours is incorrectly detecting a display addition or removal, that could explain (but not justify) the blink.
What's causing my Mac Pro Late 2013 monitors to flash black twice every five minutes?
