Errrr.... Very definitely. Have you read the manual? It gives an explanation of floating earths at the empeg which have to be tied to the input of you amp. This gives the empeg a 0V reference so that it can output without distortion. This is primarily as a consequence of the empeg being a digital based sound source, rather than pure analog.

External interference could mean that, without a shield reference, your cables are acting like antennas for all the rubbish floating around your car. The short adapter cables you are describing are meant to go between the empeg outputs and the inputs to your amp; you should then tie the earth rings to the amp grounding point. Without these fitted, using an amp with a floating or high impedance input, then you will get distortion.

The small black box saying "Amp" (which should actually say "3 Amp") is the inline filter for the power line to the empeg. Without this fitted, I am not surprised you are getting engine whine/cracks & pops.

This is cropping up over, and over, and over again. Does no-one ever read the book? Surely you must have realised that the "spare parts" were for some purpose? If this was fitted professionally, I would be going back to the shop to complain and get some part of my money back, they're rubbish....