2 days ago I had troubles with video conversion, today that's audio. Here is the problem, the converter I found (see this question) detects all my sources audio channels as different channels (like if they were dvd languages) :

The first chanenl is the left speaker, and the second one is the right speaker, all others are middle's one. When I convert my video, the output is stereo but I loose one speaker. Here is an image to understand :

I gave a different color to each channels of my source : as you can see, after output, only the selected input is used for both speakers.
I suspect this software not to handle 5.1 channels as source. Because this is the only soft I found that supports my image resolution, I need to keep it for video conversion. But I first need to convert dolby to sereo using another software.
Do you know a way to convert dolby to stereo, without altering video ?
edit: ffmpeg -i <video> command gives this output.
ffmpeg -i inputI can give an example command. – LordNeckbeard Dec 20 '12 at 3:41