Not a common problem - I know that I don't have it. I keep my 15" late 2011 connected to my Thunderbolt Display 90% of the time and let it 'sleep' when I sleep. Coming out of sleep, no flicker.
I don't know what to tell you other than to take the whole kit to your local Apple Store or an AASP and show them what's happening. Could be a glitch in the hardware, as it's not supposed to 'flicker' on wake at all.