my vague recollection of this from an older post by doug oade (or was it the sony pdf re the technology used ??)
was that tube equipment (and traditional analog transister gear) shift the phase of LF signals and that this is a part of what causes the warmer sound one hears on such gear. The phase shift (if I recall) doesn't occur on the digital amp and was added as a dsp effect by sony to compensate (again, or so I recall)
Nick -- (assuming my recollection above is even close to the mark) perhaps because the phase shift is implemented as DSP it is bypassed when run in "pure" 2 channel mode -- have you tried running your 3000es in 2.1 mode (i.e. allowed dsp to function) when a/b'ing the effect of the phase shift? If not, perhaps that's why you can't hear it?
Given Doug's repeated urgings on this issue, this sounds quite ripe for some follow-up/clarification on Doug's end