Hi Using aux on gen 2 2008 and when is plugged in to the power supply as well I get the popping sounds of the phone maintaining its phone signal , when I unplug it the signal sound stops.. I drive for 4.5 hours and use the phone for pod casts and sat nav.. Do it does need to be on charge Martyn
Solution: unplug it from the power unless you need to charge it desperately. (I also found that audio quality was very limited when both charging and using the headphone jack -> 3.5 mm aux in on my '06 via the built-in aux in on the JBL system.)
Pretty common phone issue. Wife's Toyota Sienna and my Prius both have a slightly detectable whine through the aux when charging the iPhone.
