i might know what happened... its a very strange thing that happened to me once, but its worth a try for you, i was playing 1NSANE (that game nobody has ever heard of) and at one point it crashed, after that i had to hold in my keys for around 1-2 seconds for them to actually register, what happened was some kind of windows ease of access feature was randomly turned on, the feature was for people with shakey hands or something, and i had to disable it in the control panel, i wish i remembered more about it, but it was years ago...
although its very likely that this is not your issue, im just putting that out there.