Can you solve these intermittent audio problems with Ford Sync and iPhone?
I don't have an answer, but I have the identical problem with an iPhone 3G.  The sync system will recognize USB for about a month and then start failing until it flat out won't recognize anything device that is inserted into the USB port.  I've had the guys at the dealership look at it 3 times and each time they get it to start working again by upgrading the sync software or it just happens to start working.

Have you found a solution beyond using Bluetooth?  I can't even charge my phone anymore through the port.