I might as well update my repair. They did not end up replacing my USB port, as it was also in for a oddly behaving passenger window (would roll up with the master window switch and then back itself down about 3/4 of the way). They found a bad "junction box" that seemed to be causing the USB and window problems. They replaced that in the end and left the USB alone.
As aside, this was the car's first trip to a US dealer since moving back from Germany. The SA could not really tell me if they "updated" the car (never been done previously) although they had to activate my US BMW Assist and they stated that it required extensive programming.
My SA is kind of lame. Can anyone out there that can check software version?
2009 M3 E93 Silverstone II over Bamboo: 6MT, Tech, Premium, Cold, Premium Sound, Ipod, 19'' Wheels, OEM Exhaust Mod.