I have read a few threads regarding problems with the Thunderbolt displays and Macbook Airs. None of the suggestions in there work for me including doing an SMC Reset.
Here is my problem. I have a brand new Macbook Pro 17", 2.5Ghz Core i7, 8gb ram, 750Gb HD etc., new Thunderbolt display. Running OS X Lion 10.7.3.
In the back of my display I have plugged in a USB mouse from Logitech, an Apple full size keyboard and my wired ethernet connection. The monitor and peripherals stay at work and I take the Macbook Pro home every night. If I do not follow a certain sequence every morning, my computer freezes. I put the power connector in first, open the lid, wait for the screen on the laptop to show the login prompt, login and then and only then can I plug in my Thunderbolt connector. Once I do this, my second screen lights up and my mouse, keyboard and ethernet connection works. But if I plug in the Thunderbolt first before power up or if I plug it in before logging in, then I have a high probabilty that the USB hub on the back of the monitor will stop working altogether. Then I have to move my mouse and keyboard over to the laptop and everything works great (my ethernet keeps working fine though). My mouse scroll for whatever reason goes into high gear and starts scrolling much faster and I have to slow it down.
Now, this works 90% of the time. But there are days, like today, where this process does not work. And when it doesn't, either I have to move the USB devices over or like today, the machine freezes and no longer responds to any input. It appears to still be working as the screen updates but I can never regain control of it via any keyboard or mouse.
My co-worker has the exact same setup and exact same problem. We also have 10 Thunderbolt displays here (all new) and same problem with ANY I choose. So this is not a hardware issue. Something is wrong with the driver code for some device. And my co-worker has an Apple mouse so that's not the issue either. If this can help Apple with debugging, here is another interesting tid bit. 3 weeks ago, I had a non Thunderbolt display. And for 6 months with an older laptop, I had issues with it's USB hub. Same kind of problem. Some days, the USB hub in the monitor would work and others it would go dead until a reboot was performed.
I think a driver needs some fixing somewhere.