Hmmm... Makes sense - especially given that it is an aux source...

As a reality check, you might want to put a splitter on your shuffle's output and listen in, just to make sure the track is playing back properly.

Also, what is your volume on the shuffle? Could you be coming in too loud and getting volume clipping?

Lastly, try hooking up another device (any portable source) to the aux input and see if you get the same behavoir.