I started having a similar problem. I added the Iron Cross IPOD adaptor (HDPDPLUS2) to my head unit and problem solved. That thing is GREAT, and it charges the phone at the same time. it was super easy to install, the hardest part was trying to decide were to put the IPOD/IPHONE Plug.

 

I just checked out the cable, kinda pricy. My guess is it is the old cable, but it does not specify that. I have an iphone 5 with the new lightning connector. Anyone know if iron cross has one for the 5?

 

UPDATE:
I got it fixed. Thanks to the help from this board, I found that 2 of the connection points on the aux jack were loose. I soldiered them back nice and solid, and added a bead of solder to the ground connection as well for good measure. It is working as it should.

 

Good job! Was it hard to do?

 

Hardest part of the job was getting the radio bolted back in, the rear mounting bolts are a bear to get to, especially the right side.

 

I had a missing bolt on mine from when I changed my handlebars. I don't remember which side. I gave up on it.

Later on the fairing brackets broke and I brought it to the dealer for warranty replacement. I asked them to put the missing screw in while they had the fairing off.

I later pulled the fairing for something and noticed the screw still isn't there.