If anyone cares, I think I figured it out.
Basically I think the use of a pre-amp sonos unit connected via RCA to an amplifier is a bad architecture.
I think the cause: by controlling the volume in the pre-amp unit -- dropping the pre-amp signal level to lower the volume -- it just drops too low at low volumes and the amp gets no signal. I think the design of this amp was to have inputs with a constant signal level (i.e. a CD player, etc.), and control volume through a wall mounted rheostat on the amplified signal. If it had an optical signal input, maybe it would work, but this setup does not with this particular amplifier.
I think the easy fix for me is to replace the sonos pre-amp boxes with amplified sonos boxes, one per speaker pair. Since they presumably do all this in digital, it will work -- and I came to this by experimenting with a sonos connect:amp I had laying around which works fine at low volumes. I think I did the Niles amp originally under the idea of a higher quality audio, but in practice, ceiling speakers are pretty background anyway, and not being able to operate at low volumes is a much bigger problem than slightly worse audio, in this context.
Thanks for the suggestions, the idea of isolating out the amp led to this insight. Cheers.