I agree that the symptoms you describe make it sound like a hardware problem, such as the aforementioned broken traces, or maybe a bad op-amp or bad capacitor. The fact that the audio problem is only on one of the two pairs of outputs should (under normal circumstances) be a dead giveaway that the problem is entirely in the output stage of the audio hardware.

HOWEVER... you *are* running custom software. And the DSP on the empeg is controlled by software. And the front/rear outputs do have features that are DSP controlled. So if you can't find anything wrong with the hardware, I'd say, see if the problem reproduces by running a regular player build.