What do you mean by "affected" ? Could you please provide the error code displayed when you try to update your system ?
I don't get any exact error codes. But when I search for updates it doesn't show all. I can recall this from formatting a lot before, with this CD and exact build and I'm supposed to get a lot more updates. Is there any way we can look more into this?
This may be caused by a misbehaving driver. Which operating system are you currently running ?
I'm running Windows 8.1 at the moment. Could we assume that the malware is running as a driver then?
BadUSB is quite hard to detect but is not spreading in the wild. Did you try another keyboard device ?
I haven't tried with a clean combo of new mouse and new keyboard yet. But I have tried with a different keyboard but the same mouse and it seemed like both devices got messed with in the end.
I have attached logs from Gmer and RogueKiller.