I have a similar setup and problem. My Thunderbolt display (refurb, purchased in February 2012) will randomly turn off, as if it went to sleep - but mouse/keyboard input does not wake it back up. The internal speakers will still output audio. Disconnecting/reconnecting the Thunderbolt cable from the attached Mac Mini (2.5GHz dual-core Intel Core i5, OS X 10.7.5, AMD Radeon HD 6630M ) will not resolve the issue. Disconnecting/reconnecting the display's power cord and the Thunderbolt cable from the Mac Mini will resolve the issue temporarily. This began happening maybe a month or two ago, and has probably happened 10 times in the last 30 days. It is completely random, and I have yet to be able to duplicate it on demand.
Steps taken to attempt to fix the issue:
Confirmed Energy Saver Settings
Confirmed Software up to date (OS 10.7.5)
Attempted Firmware Updates (message states not needed)
Reset NVRAM
Reset SMC (unplugging computer)
There are other discussions reporting similar behaviour:
https://discussions.apple.com/thread/3340067?start=0&tstart=0 (13 pages)
https://discussions.apple.com/thread/3352192?start=0&tstart=0 (5 pages)
https://discussions.apple.com/thread/4243396?start=0&tstart=0 (2 pages)
https://discussions.apple.com/thread/3347412?start=0&tstart=0 (1 page)
As well as other discussions concerning random flickering issues with the display.
Since I'm still under warranty, I took my display to a Genius Bar today. The rep didn't really seem to want to hear about what I found on these discussion boards. He says you can pretty much find anything you want to find here, and since it is unmoderated it is not a reliable source of information. I let him know that the issue (as far as I can tell) occurs with different models of Mac Mini's, MB Pros & MB Airs, suggesting it is in fact an issue with the display and not what's connected to it. I added that most folks who reported bringing the displays in for service ultimately ended up with a replacement display, as the service done on the defective display proved to not resolve the issue - but I would of course defer to his judgement.
He decided that they would order and replace the LCD panel. He assured me they would keep the display powered on for 12-24 hours after the service to ensure the issue has been resolved. Truthfully, I am not optimistic. And for the amount it costs to replace the panel ($833.32 from the provided estimate), I speculate this course of action will end up being much more costly for them in the long run. But we shall see!
I will be sure to provide updates as they come. Wish me luck!