Yes - typically this is a cable or grounding issue - that is that the ground connection at the head unit and the ground at the Phatbox are not
exactly the same, either due to electrical noise from the Phatbox, or from elsewhere in the vehicle (such as the alternator). The result is that this ground difference appears as a part of the signal on top of the audio.
Sometimes this can be cured by making sure that the Phatbox connects to ground only at or near the head unit (sometimes through the interface cable). But getting rid of one source of noise in this way can make another source more noticable. When I tried this I had alternator noise which I could get rid of, but I then got the digital system noise from the Phatbox instead.
Often some experimentation is needed, including possibly isolating the Phatbox casing from the mountings (if not already isolated) or actually grounding the casing if it was isolated. But I recommend that you check for any significant voltage before adding wires. You should only be able to measure tiny fractions of a volt if there is a difference.
As a last resort (but often a very effective one) you can put a ground loop isolator in the audio path from the Phatbox to the head unit. I did this when putting a VW box in my Volvo (see my wiki page for a bit more on this -
http://wiki.phathack.com/VW_Phatbox_to_Volvo_Transplant_%28How_To%29 - about half way down). This was cheap and completely successful in my case.
Les.