When using the iPod connector in the glove box I noticed it takes over and leaves you with no control of the iPod. You can only advance or go back one track at a time with the head unit controls. Additionally, after using the interface then playing the iPod later in a dock, it now mixes tracks in from different playlists other than the one selected, for instance, tracks from my holiday playlist now play in with my other playlists. Anyone notice this?

Never heard of this problem. Call the dealership and ask if anyone has complained up this issue and if there's any sort of software update available. It could very well be caused because the ipod's software is more advanced/complex than the OEM stereo causing software "corruption" from data transmission to and from both devices. The OEM adapter is probably better suited for operating the iPod Shuffle.