MediaCoder

Right now, if you try to encode with mediacoder, it won't let you select an audio track if there is more than one

You have to extract the audio files, and then encode it, then stick it back into the finished file you want in order to encode a select track

Up until build 5600, when I stopped testing the builds (see Test Reports listed under Tips & Guides), MediaCoder successfully gave the chosen audio stream. A description of the test, etc, is given in the Test Report.
Your failure may be due to the choice of Decoder/Encoder, etc.

It does let you do that, but you might need to force "video source" to mencoder or ffmpeg.