Quicktime Video Conversion Not Preserving Multiple Audio Tracks

Hi All,
I'm trying to convert a H.264 video file to a ProRes MOV using quicktime pro 7.
This is a video file that was created using Handbrake.
In Handbrake I am able to rip several audio tracks from a VOB. In this case I need to rip both the 5.1 audio and 2.0 audio. Instead of splitting this up into separate exports, I can attach both audio tracks to the H.264 mov. I can view and edit them in the Properties window of the video in quicktime.
So what I'm starting with is a video file with two Audio tracks:
5.1 Surround: C,L,R,Ls,Rs,LFE + 2.0 Stereo: L, R
What I'd like to do is unite the two audio files to create an 8.0 track: L,R,C,LFE,Ls,Rs,Lt,Rt
By changing the naming of the stereo track from L,R to Lt,Rt in the properties windown, an option appears in the audio export settings to use the SMPTE DTV audio output (L,R,C,LFE,Ls,Rs,Lt,Rt). But when I use it, assuming it will recognize my naming structure and rearrange the tracks according, the export results in a stereo file.
What am I doing wrong?? All logic makes me assume that this should work...
I should note that when I open the H.264 in quicktime the 5.1 audio track is not enables (or clicked on) in the properties tab. I must turn it on for quicktime to recognize it in the inspector window. However, when I try to save the video it requires me to save my file in an MOV container.
When I try to simply export the file as a 8 discrete channels, it will export with 8 channels, but the first two are a stereo pair and the other 6 are silent tracks.
The only way I've found to keep these audio tracks together is to extract each audio unit separately (5.1 and 2.0) and then add one of the audio tracks to the other using the copy and "Add to Movie" feature. This is not my preferred workflow since I'd like to keep the audio and video together. I'm creating a workflow that will be repeated several times so the more I can streamline this process the better.
Please help. Any ideas would be great.

I don't think Quicktime Pro is able to export individual audio tracks. It sounds like Handbrake create an AC3 sound track and a 2.0 channel stereo track. I don't think iMovie will handle multi-track audio and Final Cut Pro X won't let you assign audio channels to individual outputs.
If you have the original VOB file, DVDxDV Pro will break it out to individual audio channels into separate AIFF audio files which you can then import into Final Cut Pro 7 and remix the audio that way.

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Quicktime Video Conversion Not Preserving Multiple Audio Tracks

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