Can you solve these intermittent audio problems with Ford Sync and iPhone? Most of the time my iPhone 3GS works well with the Ford SYNC system (based on Microsoft Auto/Windows CE) in my Mercury Milan Hybrid.  I connect the iPhone to the car's USB input (inside the center console) and select "USB" on the "Media" screen.  It will start automatically playing whatever was most recently playing on the iPhone (which is usually a podcast for me).

The iPhone also plays well through Bluetooth (using the A2DP profile, I presume).  I prefer USB though because the steering wheel controls for next/previous track (and fast-forward &amp; rewind) don't work over Bluetooth (probably because iOS doesn't support AVRCP), and the volume is significantly lower over Bluetooth than when using USB.

It feels like increasingly often I can't get audio to play over USB.  I will sometimes see a message saying something like "Autoplay not supported", and it won't play if I select a track (or podcast) on the Ford Sync screen.  Disconnecting and reconnecting the iPhone doesn't help, and I usually continue to have the problem even after turning off the car and opening the door to turn off Ford Sync.  (Though usually it works again the next time I drive the car.)

When this happens Bluetooth still works, though the USB problem occurs sometimes when the Bluetooth connection drops.  I can manually reconnect the iPhone over Bluetooth, and then the USB doesn't work.

I believe I noticed these intermittent problems before I upgraded my iPhone 3GS to iOS 4.0.  But they may be more frequent since then.

Has anyone else run into these problems?  Have you learned anything I haven't?

Update: The last time this happened I turned off audio (by pressing the volume dial).  USB worked when I turned it back on.  I'll keep my fingers crossed that this works whenever USB stops working.

Update #2: Nope, turning off the audio and back off doesn't work.  If when I switch to USB I don't see the track name, then in a few seconds the audio will stop.  And I've never successfully got it to work again, without turning off the car and waiting several hours. (I don't know if it always displays "Autoplay not supported when this happens.)

I don't know whether this is related, but occasionally when playing audio over Bluetooth, the Bluetooth symbol will disappear from the screen and the audio will stop.  When I got to the phone settings, the phone I've paired with Sync isn't displayed.  If I wait a minute or two, the paired phone will be displayed and I can reconnect.

I guess I should look and see if there's an update to Sync available.

Update #3: I've noticed that sometimes when playing audio over USB the Bluetooth symbol will disappear from the my car's Sync screen (as described above).  The audio immediately stops, and won't start again until I reconnect to my iPhone over Bluetooth.  (This is somewhat annoying, since Bluetooth shouldn't have anything to do with USB.)

I like the Ford Sync system, but it appears my worries about Microsoft's tendencies towards inferior quality and lack of attention to detail were not entirely unfounded.

Update #4: I've discovered (accompanied with a face-palm) that I can crank the volume on my iPhone to max to come close to the same volume over the car speakers that I get over USB.  And I don't know if it was the iOS 4.2 upgrade (with AVRCP support—which works well except for fast-forward and rewind), but the problem I describe in update #3 has been rare lately.  So I use Bluetooth most of the time and don't subject myself to the USB problems described above.  Bluetooth has the additional advantage of starting automatically from where I left off when I start my car.
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.