Ah-HAH! Here's the deal with my files:
I did in fact have (for example) 8 mono channels comprising a 5.1ch mix and an LtRt downmix. All 8 channels passed through to avisynth discretely. HOWEVER, the trick in my case was that each channel had an actual QuickTime channel assignment - i.e. L, R, C, LFE, LS, Rs, Lt, Rt etc... Still 8 discrete tracks in QuickTime, but all a part of a big happy mix!
I guess adding the channel assignment / mapping fixes this issue? Glad to see unassigned / unmapped tracks work fine now too!!
Derek