[mzel]

We've had a similar problem in Nickel, but now I stumbled upon it in KoReader. Originally Kobo could not recognize one of the two USB ports of my laptop. A couple of firmwares back Kobo fixed it, and now Nickel connects to both of them just fine.
However KoReader establishes the problem with the same port. When you connect it to the "bad" port it says it is "power only connection"