SOLUTION WORKAROUND that worked for me > Set Energy Saver > 'Display Sleep' to "NEVER"
I used the following WORKAROUND to solve this screen-flicker/frozen/window-repainting problem on my Retina MBP:
Workaround Highlight:
Essentially, I configured "Energy Saver" settings so that the display can NEVER go to sleep. Yes this sounds drastic, but it is a workaround that works for me and really is EASY to use.
Specifically, I set the following:
1) Goto System Preferences > Energy Saver
2) Set "Display Sleep" to "Never" for BOTH "Battery" and "Power Adapter"
Since doing this, I have not had ANY problems with flickering or windows not re-painting etc. This has been over a week now of screen/display problem-free computing on my Retina MBP.
Problem Symptoms Highlight: The problem seems to happen when the Display comes OUT of sleep mode. The display seems kind of frozen and when I drag windows around the fragments of the screen flickers. I'm talking about the SYSTEM being ON the whole time and just the display going into and then out of sleep mode. (e.g. Time passes, screen goes blank, then when I do something like click the trackpad to 'wake up' the screen, the display problems occur with flickering, frozen fragments of screen and window-repainting problems/flickering when I drag windows around.)
THUNDERBOLT specific Issues: Also, using a THUNDERBOLT Port for an external display OR Ethernet cable adapter OR external hard drive seems to exacerbate the problem and the display problems then happen MORE frequently for me...as in EVERY time I come out of display sleep. So, now I just NEVER go into Display Sleep and that has fixed the problem for me in a 'workaround' fashion.
To be clear, since I started using the Display-Never-Sleeps workaround:
o I have NOT seen these screen frozen/flickering and window dragging/repainting issues at all
o I have never seen these issues/problems when coming out of SYSTEM Sleep, before or after using the workaround. These problems have only happened to me when coming out of display sleep.
When I need to leave my laptop ON and walk away, and therefore I want the screen to be blank/black to save power and/or avoid burn-in while I'm away, I simply manually decrease the display brightness to a black screen.
I know that this sounds terribly un-sophisticated....but then I did say it is a "Workaround". Once I got used to doing this (manually decreasing/increasing the display brightness because the display is configured to NEVER go to sleep) for a day or so, it became kinda second nature for me, not a big deal, and I have been able to use this 'workaround' to avoid the display problems described in this forum.
I hope this helps.