I have a Macbook Pro which I use in combination with a Thunderbolt display. I also have a standard Apple USB keyboard with numeric keypad which is plugged in one of the USB ports of the Thunderbolt display.
The problem I have is, that the keyboard is often not recognized. Usually when I shut the laptop down and start it again. I usually managed to bring it to work when I unplug the keyboard several times and plug it in again OR I open the settings and wait for some time and do random things.
I don't have any problems when I just put the Mac to sleep. The keyboard will still work when I wake the Macbook up again.
The keyboard works perfectly well when I connect it with the Macbook directly - so it seems not to be an issue with the cable. Other USB devices work in the ports of the display - so this seems not to be the issue as well.
But of course I want it to work with the display so that I don't have to unplug too many things to take my laptop away.