Just wanted to post this in case anyone else stumbles across the issue.
I had an issue with really bad digital clipping in low volume mode. I removed the HD500 from the chain and went straight into the top of the amp, still no luck. The normal volume mode seemed OK, but low not. Anyhow, I read in this forum that the low volume mode is modeled and not done via the same signal path so I thought to upgrade the firmware. I was already on 2.0 (latest), but I went for the reflash anyway. When the amp came back up again, everything was back to normal, so either the program in the flash or some settings had been corrupted.