Videos with multiple audio channels are common in media industry. The default FFMPEG parameters should be slightly altered in order to deal with these videos.
Please use the below parameter to extract all audio channels from a master video and burn it to proxy file.
Video Settings: -i "eSourceFile" -y -s 1920x1080 -map 0:v -map 0:a -b:v 1024k -vcodec libx264 -r eSourceFrameRate -movflags faststart -pix_fmt yuv420p "eVideoProxy"
Since all audio tracks are embedded to the same proxy files, only Internet Explorer can read those tracks. Please use IE in order to get the different audio track selection.