This just recently started happening to me (like a couple weeks ago).
It's weird, sinve I've been using the same setup since I got my thunderbolt display (macbook air).
I updated to Mountain Lion, but I don't thgink the issue started happening with Mountain Lion (maybe one of the recent Mountain Lion caused it?)
The issue I started experiencing is that the display won't wake up from sleep, and I need to reboot my Air for the display to work again 😟
I tried changing the settings to uncheck the Put hard disks to sleep when possible, but that didn't fix the problem.
Should also be noted that once in a blue moon, the display will wake up from sleep.
Apple, how do we get you to fix this? I don't have time to call support during the day, and it looks like you decided to shut down email support 😟