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Rob and Vumad, I have a Thunderbolt Display (TD) and a MacBook Pro Retina (MBP) connected. What I have found after a lot of troubleshooting is that if the devices are properly connected and working and the computer is allowed to sleep (computer sleep, not display sleep) or it is re-started, after re-start although there is video, there is no control via the ports on the display (USB, Firewire, Ethernet, etc.). ADDITIONALLY, you will find that there is no sound from the display or iSight/Facebook Camera function from the display (these have returned to only the computer).
I have an open case on this and am going the Apple Retail Store Genius Bar this week to demonstrate the problem connected to there MCP computer. Engineering at Apple requested I do this.
It appears that something is not allowing the TD's internal hub to be recognized after the type of disconnect I mentioned (computer sleep or re-start while the TD is connected). You can visually see this if you go to System Information and look at "USB" when properly working you will see the USB, sound and camera functions on one of the USB high-speed buses (usually the bottom one), but if the problem occurs you will see that none of these items from the display are there.
My work around is to set my computer to NEVER sleep (again, display sleep is just fine). And, if I must re-start I command a shutdown and disconnect the TD. Then after the computer is booted, I re-connect the TD, and the controls are again present.
Hope this is of some help.
Barry