Thanks for the tip. I'll give that a try. For now the unit is just sitting on the floor of the trunk. I was thinking of strapping it to the roof of the trunk, but I'd much rather get it working properly in the designed location.
Interestingly, the noise doesn't kick in until the car has been running for a few minutes. I tried tapping the ground wire on the PhatBox cable to provide an additional ground lcoation, but that didn't work either. I've never come across any car stereo equipment that was this stubborn.