Well I'm going from single-ended RCA>RCA (Matrix to Mini-Torii). and I had this same type of noise when I didn't have the Matrix but a Peachtree Nova, but then I would only get the noise (not a ground loop but direct PSU noise from PC) when connecting a DVD player to the Peachtree. I had an external 1616M sound card, not the Lynx, at the time. Same problem. I have tried so much hardware that I'm convinced these dc-dc converters have grounding issues....and they are supposed to be the last word in audiophile music servers. Wayne informed me the switching psu is to blame and of course the linear power supply is the soltution, but expensive, hot, and big.
There were times I had NOTHING connected to the PC and the noise would travel into the signal chain, when I powered down the PC, the noise vanished.