I'm also having this problem and I've noticed the following:
- The problem seems to manifest after a number of disconnect and reconnect cycles of the USB cable to the computer.
- I've been able to 'reset' the ports back to working by disconnecting it form the computer, unplugging the power on the D6000, and then leaving it unplugged for a few hours. NB: a short power cycle doesn't do it, but a very long one seems to.
YMMV. Not a fix, but perhaps the workaround will help someone...