This points to a keyboard scan controller issue and that chip and connections are on the motherboard. I would write to try another keyboard but you did that.
DO NOT CALL IT SOFTWARE YET. I always boot up another OS to be sure.
I have an X120e lenovo thinkpad running with windows 7 professional
It has some keyboard keys which do not work. I swapped out the keyboard for another - same problem.
The keys that are not working are: b n ? ] [ y t backspace
One of the odd things is that several of these seem to be paired.
The not working keys seem to be the same ones on the old keyboard
I just plugged in a usb keyboard and it worked fine so this is not a software problem!