Currently on my empeg, at a lowish volume setting I can hear *everything* that goes on inside (and outside) the player through my speakers i.e. HDDs spinning up, changes on keypresses and so on.
This is all with the ENGINE OFF, with the engine running I additionally get alternator whine.
In my case it's easy to turn the volume up past this background noise and lose it.

Like you, I also have a very good (*star*) ground wiring but am still getting the problem. I have a 'fix' available (ground the player's RCAs) separately which I will implement soon.

The point to this post is to point out that some ground loops can seemingly defy common sense and reasoning based upon sound (no pun intended) electronic experience.