I had the same problem with my new MacBook Pro Retina connected to a new Thunderbolt Display running OS 10.8.2. I did resolve the problem after a week or so of troubleshooting, but it did involve getting a resplacement display from Apple.
Here WAS my situation: After connecting the display and having things work (video and external keyboard/mouse and sound/video), when the computer went to sleep (not display sleep, computer sleep) or when it was re-started via the display, I had video but did not have any other external control or display sound/video (was as if the internal hub of the TD was not working).
When I disconnected the Thunderbolt connector (which comes from the "All-in-One" TD cable) from the computer and then plugged in a regular Thunderbolt cable to the computer port and the empty TD Thunderbolt port, all was well. In other words I left the TD Thunderbolt connector disconnected and bypassed it with another Thunderbolt cable between the computer and the TD display port. Note that I left the power connector from the "All-in-One" cable connected as there was no problem with that portion.
This, of course meant that the Thunderbolt part of the All-in-One cable (which is not unpluggable from the display) was bad or the display electronics leading to it was bad. Either way it required a new or repaired display.
I hope this is helpful. After bypassing the All-in-One Thunderbolt interface with my workaround above, I never had the problem occur again (you could command the computer to sleep or re-start it from the display, remove the laptop to use elsewhere, re-connect it, etc. and everything continued to work without fiddling with any connections). As a result, I had Apple replace the display under warranty provisions.
Barry