I guess I might have ground loops. And I think they might come from the connections between my MB6582 and the filter box.
The filter box contains PSU, AOUT_NG modules, SSM2044 modules and SSM2164 modules. Connections between the box and the MB6582 are:
PSU - (+12V, +5V and GND)
Expansion port - (link to AOUT_NG, 3 wires (GND and +5V omitted to avoid loops) and one digital out for bypass relay.
Audio - Audio jacks out from MB6582 connected to audio jacks in to the box (L, R, GND)
So there is a separate ground for each audio channel in addition to the PSU GND. Should I just cut the GND for the audio connection?
The same question arrises for the CV connections. GND is connected once more for each CV in addition to the power supply GND.