5.1 AC3 downmixing to stereo

Hi,
I am currently working on a workflow to create my own AVCHD discs (Blu-Ray on a DVD-R) from my Sony SR11 without editing or transcoding in Premiere. I import the files directly into Encore after demuxing them using tsMuxer (I need to demux them first because for some reason, Encore will refuse to import my muxed stream complaining about too many audio channels). The demuxed sound files are 5.1 AC3 Dolby files. When I create a timeline in Encore and add one of my video/audio file, the generated audio in the final disc is Dolby 5.1. However, if I include more than one video/audio pair, the program goes through a short transcode stage and the audio is converted to Dolby Stereo on the generated disc.
Any idea why?
Darth

This is my second BD title that I've authored in Encore CS3 and this time around, I am having the same problem with Encore mucking with my 5.1 .ac3 file and converting it to 2 channel PCM. HOWEVER, I am not trying to join .ac3 files on one timeline. I have a dedicated timeline for each program on the disc.
I went back into the Project tab to see what the status was, and I see it shows "transcoded" so I changed the asset to "do not transcode" and burned another image. Unfortunately, Encore sabotaged my audio again, and there goes another $21 BD-R disc--the audio shows up as 2 ch PCM on the Sony BDP-S301 player, NOT the original 5.1 AC3 Dolby that was encoded from the DVD version of this program.
I don't know what is different about this project (I could have sworn my previous project containing a 90-minute concert left the AC3 audio in surround format) but I can't seem to feed it surround audio anymore and have it remain UNADULTERATED by Encore. Setting the attribute to "don't transcode" is apparently a joke--Encore ignores it and just does what it wants. I find a 1 GB .wav file in the transcoded files\ folder after each disc rendering session.
More perplexing is that on a prior BD I authored last year, I didn't have to do anything to the flags--5.1 ch ac3 remained intact and Encore seemed to know enough to leave it alone. But now it transcodes all ac3 audio to 2 ch PCM and I'm burning through an expensive and precious supply of BD-R media, trying to achieve a disc with 5.1 surround, as the original source files provided to Encore are.
I'm at wits' end. This is just one of a slew of things I hate about Encore, which reminds me a lot of editing in Dazzle's DVCII MovieStar application on a Pentium 400--glacially slow at repositioning in the timeline, garbage quality previews that don't manage even 1fps at 12 dots per inch, unstable, and always out of memory. How I long to be authoring in Scenarist BDMV!

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