Wouldn't that indicate something between the amp and the speakers?

Not necessarily.

Noise problems, especially when caused by grounding issues, can be caused anywhere along the power/signal chains. You really have to examine the whole system carefully, step by step.

Did you print out those PDF documents about noise? Those are very useful and accurate, and would be great ammunition to give to your installer. One of them has a very specific diagram of how to use a relay to get rid of exactly those sorts of pops.

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Tony Fabris