I just updated my iPhone 3gs to 4.0 software.
Totally usless in the truck now. USB does nothing, will not charge, will not do anything. The first time I plugged it in it connected for a minute and then said "Device not compatable" Now its totally bricked.
Have not tested bluetooth out yet. But this is a major bummer I can't charge or do anything with the iphone in my truck.'
Pull the fuse for the sync system - turn the truck on. Then turn it off. Replace Fuse.
Others have had your same problem and this fixed it.
FYI, I had problems with my 2010 GT500 with Sync and my 2010 Raptor with Sync. I had my Iphone 4 (new hardware) paired wirelessly in both vehicles. The first time they were paired, nothing worked. After shutting down each vehicle ONCE after the first pairing, both vehicles worked fine with bluetooth pairing.
I know that is different than the USB debacle, but try pulling the fuse and see if that resolves the problem. It resets the module that controls/talks to the USB ports.