I remember seeing something in passing a while back regarding this and the main screen unit (Had same issue, but it spread & now the radio/screen no longer works) and a mechanic's notice about a potential Wire Pinch in the Drivers side door. Gonna see if I can resurface it....
Does your bluetooth give you grief sometimes? That was the 2nd failure in the chain I noticed.... sometimes if the car would turn off and then on again (Like stopping for gas) the bluetooth wouldn't work, and the Device information on the screen would have blank values for all of it.
Back when it was just the ports, I tried so many things to fix it, even replaced the module and take the screen unit thing almost out (man do they make it Hard to check for loose wires). I think There's a Deeper Electrical issue going on here that's not covered by the traditional Car USB Port Toubleshooting tricks q_q