First ensure you have the latest Version of SYNC 3 installed.
I also found that the USB ports would only charge my Black Berry intermittently, disconnecting every few seconds.
I have been trying to install the new Sync update without success.
Not sure if it's software, the car's USB ports or the two particular thumb drives I've tried.
If voice guidance, nav commands and Gracenote data are updated, too, installation process might take 80 minutes or more.
Get in your car, start the engine, put your USB thumb drive with the maps upgrade in the front plugs, start driving around for a while, and follow the instructions which will show up on the screen every now and then: After Installation/Upgrade procedure is finished it is always a good idea to perform a full shut down/off procedure or even perform a master reset on the apim.