Ground Loop (courtesy of Wiki:
http://en.wikipedia.org/wiki/Ground_loop_(electricity))
Low current wiring is particularly susceptible to ground loops. If a signal is passed from one to the other via an audio connection with the ground wire intact, this potential difference causes a spurious current through the cables, creating an audible buzz at the AC mains base frequency (50 or 60 Hz) and the harmonics thereof (120 Hz, 240 Hz, and so on), called mains hum.
The first solution is to ensure that all metal chassis are interconnected (think fat 0 and 1 AWG ground cables), then connected to the electrical distribution system at one point (often referred to as a "single-point ground"). Another solution is to use isolation transformers (aka ground loop isolators to avoid a direct electrical connection between the different grounds. The better isolation transformers have grounded shields between the two sets of windings.
An isolation transformer is a transformer, often with symmetrical windings, which is used to decouple two circuits. An isolation transformer allows an AC signal or power (signal, in this case) to be taken from one device and fed into another without electrically connecting the two circuits. Isolation transformers block transmission of DC signals from one circuit to the other, but allow AC signals to pass. They also block interference caused by ground loops.
So, thats a long winded way of saying that the ground loop isolator will not fix the grounding problem, it just takes it out of the equation for the audible signal path (RCA's between HU and amp). The affect on SQ is minimal, but you would obviously be best off taking a long hard look at how your grounds meet the chasis, how your negative terminal meets the chasis, and how the chasis is bolted together (again, think big 3).
Hope that helps!