Well I don't know for sure that the source of the hiss is the Phatbox or not. It could very easily be the HU itself. Lacking any specs on it, I would not be surprised if the signal to noise ratio isn't very good.
Yes, the EQ is installed after the HU and I will try the ground loop isolator there before I try anything more ambitious.
But since the HU (and Phatbox) both share a common ground while the remainder of the system share a different ground (in the trunk for the amps) maybe the ground loop isolator will work.
However, I have experienced ground loop problems at home when connecting the output from a PC to a stereo at the other end of the house. The noise was not hiss, but a definate "hum". So I am a bit surprised that this hiss would even be considered a ground loop problem.