One day, I noticed there was a slight scratchy noise when I plugged the headphone jack into the Aux-in socket. I pulled off the panel to see what was behind it and noticed that the jack was not firmly attached to the panel. I tightened it up. However, I had not experienced anything other than a slight wobble in the connection. It worked fine before and after.
I have the factory installed Aux-In (2007) and a basic business radio.
Whether or not my iPhone4s is charging (lighter USB adapter charger), the Aux-In continues to work.
Perhaps the configuration of the Aux-In is different in factory equipped cars like mine.
It would seem odd if this was the case.
Or perhaps earlier i-devices cannot provide a signal to the headphone jack while charging. I would be surprised if this was the case too but I'm new to Apple.
From what you have said I would suspect your Aux-in connection is intermittent - a loose connection either at the radio end or the jack end. Start with the jack end. Easy to rule this out.
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