Using an LD MK III with an iphone dock

i've been using my mk III for a few hours now and i've noticed a few things. one when using my iphone with an apple dock i get a clicking or diginoise sound. i do not get this noise when i use the headphone out. this does not happen when i swap out the iphone for an ipod. with the ipod in the dock it is silet as anyone could ask for and sounds great. my questions is why would the iphone make these noises solely when used in conjunction with the dock. the dock does sound much better than the headphone out. any suggestions? i'm using an audio art 1/8 to RCA. thanks