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Hello, do you have the device plugged in when trying to use aux?
Once the vehicle failed the self test I would suspect the issue is the audio control module. Usually it can be reprogrammed to correct conditions like this. It is also possible the line in connector is unplugged as well. I would make sure it's fully plugged in. If it is I would have the dealer update the audio control module and this should correct your concern.
The connector I am referring to is the end that plugs into the auxiliary cord. I have seen a lot of people disconnect this and forget to reconnect when putting things back together. Reprogramming will vary based off your location. My dealer charges 60 for module programming. If you live near a lot of Ford dealers I would call and ask what they charge for module reprogramming.
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