Look at the way all your usb devices are connected by what type of usb cable or extension. One by one. What I found is this:
I own the older Apple plastic extended usb keyboard which came with an Apple supplied usb extension cable. Currently I don't use the plastic keyboard, my wife does. I now use the Apple aluminum extended keyboard BUT without the Apple supplied usb extension cable. I used for years the extension cable associated with the plastic keyboard. I've always had minor usb problems but wit the newer Macs, i.e. TB2 , etc now my externals get ejected needlessly, thunderbolt Display shows one half screen, OS X does not complete it installation, mouse pointer jumps randomly, thunderbolt Display stays black, etc, etc
I spent one entire day working with the two TB ports on the rMBPro and connecting only one device at a time then restart and sleep and wake. I then isolated the problem to each TB port independently. The root cause was the use of the older Apple supplied usb extension cable with the Apple aluminum keyboard. Comparing both extension cables, there is a difference. I've always wondered over the years why the newer usb extension cable never fit the plastic keyboard but the older usb extension cable did fit the aluminum keyboard. It does but now I realize too loosely.
Maybe this story of experience will open some thoughts as to your setup problem. Since i've corrected this connection issue I have ZERO issues.
