The grounding issues with my Zen Can have magically fixed themselves. I can now run the Zen stack balanced without the RCA plugged in without issue. I have no idea why.
I upgraded to the Zen-Dac-Signature and just heard the ground loop. It turns out it's not the Zen-Can amp - but actually the balanced 4.4mm lineout socket on the Dac. The alignment must be slightly off and the poles don't quite align and you can hear the buzzing hum - but push the jack right or left - or pull the jack out a tiny bit and it goes away.
(Edit) I just pushed in the the back panel on the case and it now feels like the 4.4mm Jack is clicking in more securely. I think the back panel was not seated correctly and was preventing the jack from going in all the way)
The Siganture-Dac does sound better than the regular iFi Zen-Dac particularly in the highs, it's definitely cleaner and has more separation.
I bought it as an open box from Amazon for £217, so I have 30 days to return it - but if the issue does not come back I'm going to keep it as it sounds really great.