it is almost certainly a grounding issue. I have this same problem in my car at the moment, and the only way i could rid the noise was through an in-line filter. As best i could tell the reason that you werent experiencing it while it was outside of the vehicle, is because it was not all being powered directly from the source. for example:
In my car i have a carnetix p1900, mac mini, amp, and a factory amp.
when i hook the mini up to the stereo i get noise. Now if i hook my iphone up i get no noise whatsoever. However, if i have my iphone hooked up and then plug it in to a power charger in my car, i get noise again. essentially when the iphone was running separate from the rest of the systems power/ground circuit there was no noise. In my case i am skeptical of the p1900's ground somewhere but have been unable to locate a good enough one to eliminate the noise.
i have read several articles on the best grounding practices. Some say to ground everything in the same spot others say ground independently of each other. I would try both and see if you can come up with anything better.