I do not use Windows, so I can't help you there; but hardware-wise, some USB 3 chips have issues if directly connected to an ATmega32u4, or any other USB 1.0/1.1/2.0 device. Putting an USB 2.0 hub in between seems to solve the issues. Could you try and see if that solves the problem? It could also be a cable issue; maybe the cable was squished or twisted or otherwise damaged enough to have electrical connection issues in the data lines.
I am using a short cable-type hub, with different connectors on the other end. I have microcontrollers with both Mini B and Micro B connectors, so it's quite useful anyway.