OK, fixed! After a lot of back and forth with Schiit, finally it came down to them suggesting I first plug the wall wart into power and hooking USB up to the power USB input (closest to outside edge), THEN hooking USB from computer to the Modius data port. I now have full operational excellence with audio from all outputs.
In my defence, reading their online troubleshooting, it isn't explicit that you would hook up the power port AND hook up the USB data port at the same time. While they do say power comes from USB, it sounds like the USB power is only used if you want to use one of the other inputs NOT USB. Apparently, when plugging into the power USB port, it disables the power feed on the data USB port. Now I see this:
A lot of phasing about to get it sorted, but done now and sounding great. I'll be figuring out a small riser so I can put my Valhalla 2 on top of the stack using the RCA out from the Lokius. Eventually I will replace the BOSE speaker system with hopefully some Genelecs and I will be pretty much done for a computer system.