Hey HoustonRide. Im a tech at a ford dealership and I literally fix everything with the cars including the SYNC and audio systems. So I wanna shed some light on this subject for you and everyone else. The problems you are having with the system have nothing to do with your navigation or audio system ironically enough. You concern is going to be related to the SYNC software system and module. SYNC is one of the more complex systems in the car and has had issues because it is threaded into so many systems in the vehicle. So when something isnt working right it can affect multiple things in very odd ways. For example I have seen loss of phone connectivity, random songs playing when the car is shut off, touch screen lockup, loss of apps, system settings being loss, excess song index times, songs playing randomly in phones, ect. Now, what does the system consist of? The system relies on the high speed area network (CAN) for module to module communications, the SYNC software, and the all important APIM.( Accessory Protocol Interface Module) Thats it!
So lets simplify this even more. You are currently up to date on the latest SYNC software level......so it cant be a software issue.
Although it is possible to have a wiring issue in a new car, I doubt it applies to your situation for reasons I dont want to get into at this time.
What"s left? The APIM...........The APIM is where the SYNC software is stored and run. If that module isnt operating correctly it will effect everything connected to it like your nav, audio, and phone systems.
Im willing to bet the dealership will have to replace the APIM to correct the issues you are having. Im a no ******** kinda guy and im very confident in my diagnostic abilities. Unfortunately though, not everyone else is like that. The APIM is about $1000, alot of tech's dont want to commit to something that expensive on a warranty and be wrong, so they are gonna try everything else they can think of before replacing it. In addition, there is a Ford prior approval program for all dealerships on SYNC modules which means again they wanna make sure you have exhausted all options before module replacement.
Anyway, lemme know how it goes and if you have any questions just ask.