I have a new MacBook Pro Retina and new Thunderbolt and I am having an almost identical problem. I have found any number of sequences of plugging and unplugging the keyboard to get it to work. Today, for example, I got the keyboard to be recognized by the Thunderbolt by unplugging it and plugging it directly into the MacBook Pro, then plugging it back into the Thunderbolt. But nothing so far seems to work every time.
I have also discovered that a number of other people are having problems related to getting the Thunderbolt to recognize equipment plugged into the USB ports when a MacBook Pro or Air is first connected using the Thunderbolt cable after a period away.
Today I plan to call support and try to get a definitive answer from Apple as to whether this is now considered a known problem that requires hardware replacement.
Hi there, the problem is quite easy to fix. The wireless keyboard and trackpad do not connect to your TB display directly. They connect to your Macbook Air. It sounds like you haven't connected them to the MBA.
The TB display does not have Bluetooth to connect to these devices (this is called pairing).
To get this to work properly, you need to enable bluetooth on your MBA (System Preferences, or up on the taskbar), then use the Setup Bluetooth Device wizard to connect the trackpad and keyboard to it. Verify that they work, then connect the power adapter to your MBA, connect the TB display (it should come on) then close the MBA lid.
The TB display should stay on automatically. If the MBA goes to sleep you can wake it with wireless keyboard or trackpad just by clicking or pressing a key.
Important though - your wireless devices must be on and paired with the MBA, and you need to have the MBA power adapter connected to use the TB display with the MBA lid closed.
This guide from Apple should help you as well:
You're using a wired keyboard so it's not the same issue as this topic is about, but the USB port issue is a known one.
Check out these discussions:
I was in fact trying to pair the keyboard and trackpad to my MBA, but that wasn't working. My MBA could not discover either. Many reboots later and another set of new batteries, and a few days away, today I finally managed to get them to pair. I still can't figure out why they would not pair, but hey, it's done now, so that't the main thing.
One wierd thing that happened was that the bluetooth set-up for my keyboard kept telling me to check my device and enter a password, but my device (MBA) did not ask for or provide any place to enter a password. I had to try all the different password/no password options multiple times, and enter various passwords (but with no dialog box or field showing), and finally it worked. Not exactly a replicable process...
Thanks for your advice.
I'm back in productivity mode...