Just FYI to y'all....
I had mid-2011 15 inch MacBook Pro and now I have Early 2013 MacBook Pro 15 with Retina display. At my school library we have about 20-30ish Mid-2011 27 inch iMacs (we also have LOTS of late 2012 21 inch and 2011 21 inch).
Whenever I go to the library, I always hook up my MacBook so I can have more room to work on my stuff(via Thunderbolt cable) to the 27 inch iMacs. EVERYTIME, the display does this black blinking thing multiple times a day. It's not just one iMac. I think I've tried all the 27 inch iMac we have here at school and they all do the same thing. When it's blinking in black, my MacBook screen remains unaffected(it doesn't blink at all). It wasn't so bad when I was using the mid-2011 MacBook but after I switched it over to rMBP, it just got worse. But, when I use the iMac without connecting it to my Macbook, it works perfectly without any problem.
So I try to connect it to the smaller 21 inch iMacs(both mid-2011 and late-2012 model) and I think I had this blinking problem only once while using it for over 1 and 1/2 yrs (combining both MacBooks). So far, looks like 21 inch models don't have much compatibility issues with TDM.
First, I know it's not the cable. I went to the Apple store and told them about it and they just exchanged it with brand new one out of the shelf right away.
Second, I highly doubt that 27 inch iMacs are defective. I mean there are roughly 30 of them here and all of them do the same thing.
Third, I also doubt that it's my MacBook's problem. If it was my MacBook that was the problem, then it would blink badly while it's connected to 21 inch models as well.
HOWEVER, one very interesting thing I've noticed is that it seems to blink the most when the mouse usage is high. Especially when I click often. As I was typing this for about 20-30ish minutes or so, it didn't blink once. Normally, it would blink at least once every 10 minutes or worse.
I have a confident feeling that there's an issue somewhere in OS or the Thunderbolt firmware. Maybe it's not pushing enough power(or something) for this resolution due to faulty firmware setup?(Not that I'm saying that Thunderbolt's theorethical bandwith can't handle this resolution. I know it can handle this resolution with a breeze.) I mean I'm no Apple Engineer so I don't know exactly what the problem is, but like I said I have a good feeling that it's not the hardware issue. At least in my case.