I have a video with multiple audio streams (2 channel AAC & DD 5.1) and I selected mp4 passthrough. In the GUI I then selected both the first and second audio streams but when encoded it only had the first stream (2 channel AAC). I then ran it again with just the DD 5.1 stream selected but it still outputted the video with the first audio stream. I'm not sure if the GUI is broken or if passthrough only supports the first audio channel. It would certainly be nice to be able to select the specific channel or channels.