A different approach
Call me nuts - but here's my current "logic" on this (sorry...)
Currently, the Handbrake Pro Logic II setting does not encode the .1 (sub) channel. This really bummed me out, because I didn't do my homework, and encoded most of my DVD's before actually being able to hook up to a new surround AV receiver. So, when I noticed things were sounding flat, and specific examples of heavy rumble that I knew by heart that were simply not there - I had to re-group.
PROBLEM 1: No sub woofer for Handbrake's Pro Logic II - bummer.
PROBLEM 2: 6 Channel Discreet setting preserves the individual channels, but is converted to a stereo signal through the TOSlink cable. Bummer.
HOWEVER:
My receiver's Pro Logic II setting converts that stereo stream back into surround. No, it's not digital to be sure, but the matrix INCLUDES the Bass frequencies that handbrakes PLII converter leaves on the cutting room floor.
Since I started re-ripping my collection with the 6 channel discreet setting - all the new rips have a heckuva lot more oomph. And I don't think it's only because the discreet setting defaults to 384k for the channels, as opposed to the PLII maxing at 160k - I really think there is much more bass brought to the viewing party by using this 'round about method.
As I said - call me nuts, but that's the direction I'm taking. Not perfect, but much more satisfying than the PLII setting. It does add another 10% or so to the files with the higher audio bandwidth, but hey, that's why we've bought those nifty terabyte drives, right?
