It's strange how this only occurs when Windows itself boots. It's almost making me suspect some kind of malware is at work. Have you tried using different USB ports?
Yes, I have used ever single one on my computer. All of them is blacked out when Windows starts.
I guess I could tell that I have Windows 7 64bit.
I just noticed that my internet is also gone, on my router it can't detect that it's connected to a computer.