I am having this exact same issue with almost the same exact 15" Retina MacBook Pro connected to a 21.5" iMac in Target Display Mode via Apple Thunderbolt cable. I also have a 24" Cinema Display that uses DVI/Mini-display port connected using the second Thunderbolt port on the MBP. Please note, this blinking black screen only happens on the iMac -- it does not happen on the cinema display at all.
- Retina 15", Early 2013
- 2.7 GHz Intel Core i7
- 16 GB 1600 MHz DDR3
- NVIDIA GeForce GT 650M 1024 MB
I have tried to resolve this issue via the Automatic Graphics Switching feature and other Energy settings with no luck. It definitely happens during GPU intensive work like photo editing in Aperture and video editing in Final Cut Pro X. I use a USB 3.0 hdd (WD My Passport) to store my media externally when I use Aperture and FCPX.
Would LOVE to find a solution to this because it is a bit disconcerting that a brand new (I bought the computer only a few weeks ago) MacBook Pro would have this issue.
A good friend of mine has a Mid-2012 15" Retina MacBook Pro and has two 27" Apple Thunderbolt Displays daisy-chained and has never once had the screen blink black.
He recommended unchecking the "put hard drives to sleep when possible" -- I'm going to try that this afternoon when I begin some editing work in FCPX.
Not sure if this is related to the blinking black screen issue, but I also noticed that when I'm moving my cursor over a link on a webpage, the arrow/hand flickers back and forth constantly.
Also, when I open my MBP out of clamshell mode after being connected to the two monitors, on occasion it will have a black screen -- not the black screen you get when it's powered off but it's a visible black screen that's being displayed by the GPU (I assume). The Apple logo on the back of the screen is illuminated, closing the lid and re-opening doesn't make it go away, re-connecting to the monitors doesn't make it go away -- I have to force the computer off and turn it back on.
What I notice next is that the battery life is drastically reduced on the computer. All of a sudden it's showing a half-charge on the battery icon but it's saying it's got only 2.5 hours of life remaining when it should have 4-5. So I do a PRAM reset and when the computer restarts and calculates the battery life, it's back up to 5.5 hrs.
I'd be curious to know if you're having any of those issues as well.