Thunderbolt display-connected keyboard fails to wake MacBook Pro

I'm having intermittent problems with my keyboard when I use my rMacBook Pro in clamshell mode attached to an Apple Thunderbolt Display. With increasing frequency, when I sleep the Mac, close it and attach it to the display, I cannot wake up the computer using the Apple keyboard that is attached (USB) to the display. Unplugging and repluggin the keyboard does nothing.
I can wake up the computer with a Bluetooth keyboard & login (screensaver), and the Bluetooth keyboard continues to work fine. Nut the wired keyboard never works.
However, if I simply restart the Mac, the display-connected keyboard always begins working again.
I belive this rules out a hardware problem, but I'm open to suggestions. (It's happened repeatedly—maybe ten times over the last several months. But with increasing frequency.)
I can post console logs if that would help.
Any ideas?

Clinton,
Thanks for your interest in my question. I actually own a 27" Apple Thunderbolt Display, which works with other Retina Display Macbook Pro, but not mine anymore... That's why I suppose the problem comes from my laptop's thunderbolt ports.
Any clue?
Thanks very much in advance.
Dominic

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