What you describe is exactly what I experienced when connected to the Antimode 8033 (the KEF went into standby well before the B&W PV1d), but not when connected to my RME ADI-2 DAC, or now to the miniDSP2x4HD. The KEF sub is the culprit, and apparently it has something to do with the grounding. It occurred both when the KEF turned into standby and when I turned it off completely. Unfortunately nobody had a suggestion about how to deal with this. In my case it was loud enough to make me worry that I would damage the PV1d sub.
So, the KEF "sending" the pop back via the RCA is definitely not a good thing.
But I think the issue you and I were having is that our two sub-out RCA's were not independent.
In the antimode I see two RCA outs with phase 0 / 180, so they probably use almost the same circuitry.
Were you using both, or did you use an RCA splitter out of one?
In my Denon X1500H, the two sub-outs are cosmetic, as they get the same signal.
The RCA outs on the miniDSP and the DAC are independent, right?
And in my amp, only the other sub was popping, not the main speakers (that would have freaked me out to the point of returning the KEF).
Not a good look on the KEF sub though... nor on identical RCA-outs.