I have the exact same noise with my Belkin TuneBase. I ran my cord through the ashtray where it plugs right into the line out jack on the TuneBase. Now my Ipod is positioned perfectly, gets charged, and is direct-connect line out, but I get that annoying whine.
Doesn't do it when plugged directly into the Ipod, and it didn't do it when using the TuneBase as an FM transmitter. Would love if someone had an idea for a solution.
BTW, the whole aux-in package was done very well. Good workmanship and directions. I only had one issue with installation. There was a ground wire connected to one of the bracket screws on my radio. The screw would not come out, I ended up stripping it. I just clipped the wire and then connected it to a different bracket screw upon reinstallation. Not being able to remove that screw meant I had to bend the bracket to clear the top cover on the radio. Not a show stopper, just a speedbump along the way.
Thanks for putting this together, it is sooooo much better than the FM transmitter, and a steal at $35.
Oh, and it took me about an hour and a half, start to finish. Probably could have done it faster without the stripped screw issue and having to be sneaky because I was still at work.