Hi Niels,
The power situation is fairly complex and there could be more than one source of noise. Some setups have no issues, some do. With MIDI obviously we have optoisolation so things are different there.
The power distribution in the SEQ could be better e.g. by improving the return current path (certain Molex connectors on the lemec boards/USB PCB are meant for this). I think that the LED matrices introduce some digital noise as they switch. I'm not sure if this the source of your noise or whether it is the more commonly observed phenomenon encountered when connecting USB