The sub-panel is connected by the hot lead and has it’s own ground including a second grounding rod.Lowrider, my understanding is that a sub-panel should have hot, neutral, and safety ground all wired back to the main service panel, and safety ground (which may or may not be connected from the sub-panel to earth) should only be connected to neutral at the main panel, and NOT at the sub-panel. (Jim/Jea48, correct me if I’m wrong about any of that). Is that how your sub-panel has been wired?
More relevant to your issue, though, have you tried powering the entire system from just one of the dedicated lines coming from the sub-panel? I realize that installing the sub-panel and using its two dedicated lines lowered the noise floor substantially. But using separate dedicated lines for digital and analog components, while certainly beneficial in many cases, in some cases can cause or contribute to ground-loop related noise. And perhaps the improvement the sub-panel installation provided occurred mainly as a result of the new wiring, rather than having separate dedicated lines for digital and analog. Especially if the type of wiring was changed when the sub-panel was installed, as there are several ways in which wiring type can affect noise issues.
Best regards,
-- Al