Find out which track the audio you want is, then adjust the atrack parameter. -1 will call the first usable stream (so more than likely audio stream 1), but to be more specific 1 will call it also, and 2 will call stream 2. You can't use -2 because it won't work.
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FFmpegSource("video.mkv", atrack=2)
or you'll have to demux both audio streams, ID which one's the right audio, and convert it to WAV. Then, like so:
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video = DirectShowSource("video.mkv",fps=29.97,convertfps=true,audio=false).TDecimate(mode=1)
audio = WAVSource("audio.wav")
AudioDub(video,audio)
Having to do the AudioDub routine is a necessity simply in cases where there's two or more audio streams which need to be distinguished - I'm not aware of an option for DirectShowSource which will distinguish the correct track like FFmpegSource'a atrack function can. If you don't want to go through that, use mkvmerge (part of the mkvtoolnix package) and run the MKV through it, making sure to disable the audio you don't want. It'll output a new MKV file, and just use the scripts in my last post to handle it.