MacBook Pro Retina with Thunderbolt Display Issues

I have issues when connecting my MacBook Pro to the Thunderbolt Display when I don't do a fresh boot of the MacBook Pro.  It doesn't happen all the time, but when it does, the Thunderbolt Display usually turns on succesfully, but none of my USB devices (mouse, keyboard) respond and when I try to disconnect the Thunderbolt, the MacBook doesn't realize it's been disconnected and thus I'm just left with the background screen and have to shut it down by holding the power button for a few seconds.
With a fresh boot, everything works fine.  Are you supposed to have to shut down and restart everytime you hook up this monitor?  Has anyone had these issues?

I have the exact same issue. I hauled the TB Display into the Apple Store 3 times and finally they replaced it. Come to find out this new one has the same issue still. So It has to be rMBP related at this point. Unfortunately I don't think I have it under warranty still and the issue is hard to demonstrate. I recorded videos of it but every time I go into the store and plug it is the same as switching the speakers from internal to external and it takes 30-60 mins before it degrates to scratching sounds.
Please let me know if you ever foudn a solution. Im going to try to keep taking it in until I can get this resolved.

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