I did some quick internet searching for known issues about the aux input, that is available as an accessory from the dealer. I did find some threads describing a similar problem with having the aux input temporarily ceasing function.
I currently have the aux input that I was so inclined to install myself. The install is as easy as it gets, just plug it in the back of the head unit and that's it. Anyways, with the aux input, I typically use my third generation ipod. I keep the volume set at about 80 percent and the aux input level at positive 3. This setting is made on the head unit itself once the aux input is plugged in. Every once in a while, I charge my ipod with belkin ipod car charger or the griffin power pod. My set up is not very complicated and it get the job done. I am very happy with the sound quality and its relatively inexpensive.
Apparently the power going into the ipod via the car charger is a bit too much at times. In fact after the 7 hour drive to KYI pretty much tried every possible culprit it definitely is the charger that charges the ipod. It only happens when the ipod is being charged and it has more than about 30 percent charge. The reason I say that is because when I had a fully charged ipod, not connected to a car charger, the aux input worked flawlessly. As soon as I connected the charger it would cut out and the aux option on the head unit would not appear temporarily. I then tried it with a completely drained ipod that was connected to the car charger and the aux would work fine for about 40 minutes. Then it would give out again.
I'm no electrical engineer but my mind tends to seek a logical cause to a given problem. Given the results of the numerous little tests I conducted over the long road trip, my conclusion is that the ipod, after being charged from the battery being dead to about 30 percent, can no longer absorb enough current and therefore spits out the excess out the audio jack. It seemed to be consistent when I would play certain tracks with the battery fully charged and the car charger connected that the aux would cut out. And later with the ipod recently drained and connected to the charger, the aux would work fine while playing those same tracks.
According to the threads the solution is adding a grounding loop, readily available at radioshack. I will give that a try and let you know how that works. It is certainly annoying that I cannot charge my ipod to full capacity without the aux cutting out. But at least there is a good solution already known.
The aux input is available from outmotoring.com
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