Encore transcoded audio into mono instead of stereo!!

OK here is my workflow:
Shot 1080p video on Sony XDCAM PMW-EX1 with stereo audio track. Imported footage using Sony XDCAM Transfer (makes .mov files). If you open the .mov files in QT Player they show as having Track 1 - Video, Track 2 - Audio (left), Track 3 - Audio (right). I then used QT player on most of these files to set in and out points and then copy the selections, saving them into referenced movie files. (Did not do this on all of them though). In QT Player, all of these movie files play fine. Dragging the movie files into Peak 5.2 you can see they have a Track 2 and Track 3 for the audio (stereo!).
Then I dragged all my movies (referenced and non) into Adobe Encore CS4 and selected everything and transcoded it all. (I dragged it to the timeline befoer transcoding.) The timeline shows just one audio track. It's the audio track that appeared when I dragged and dropped the video from the bin into the timeline. Should I have made a second audio track before dragging and dropping?
Because when I did Build, and it made the BMDV folder, then I burned that to a BD-R, and played it, it's in mono. All the AC3 files are in mono (left channel only). Why would that happen? Shouldn't it automatically get both channels of the sound and do stereo, or warn you before burning if it's in mono?

You are correct, sir. I'm surprised the software is not intelligent enough to recognize that. It really should be drag-and-drop simple. It should at least ask the user, "do you want to discard one audio track?"
To solve this I tried the following: go into Final Cut and export the audio as stereo AIF, then drop that in. I wanted to avoid having to re-transcode all the video, but when I did this, it decided to anyway, then had an error. So I deleted the transcode folders. Then I went to transcode again and now it's saying "Error Creating Transcode Folder" or whatever. Sigh.
This program just seems too finicky and not very robust. I'm going to upgrade to Final Cut Studio 7 and just use Compressor 3.5, which finally can export a BDMV folder that I can just burn to whatever.

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