MKV Conversion Issue: No Audio

[JonnyPhoenyx]

Hey gang, I have a MKV file that has 2 audio tracks, and 2 sets of subtitles. (Japanese/English perspectively for each)

I'm a Mac user and use Final Cut for editing. So, I need to convert these to an editable format with English audio and no subtitles. No problem! I whip out my handy-dandy MPEG-Streamclip and the MKV Converter Applications. (Using MKV Conv to convert to .mov files (h.264 codec) and MPEG for a Final Cut friendly codec (Usually HDV 720p24. No problems.)
Never had a problem before with this method on previous projects, but this time, when I exported some test clips....the audio was missing! I tried selecting a different audio track to convert, but strangely, only two are listed in both programs (as track 2 & 3, strange since there are only 2). One of which is Japanese and the other is blank. Neither gives me the option to use subtitles. Weird....

So that's my situation. My questions:
If you're a Mac user (or have experience), have you encountered this issue before?
Is there any Mac compatible software that will allow me to Select the English track for conversion? Or maybe just delete all but the english tracks. this would not have to convert to FCP friendly codecs, just something other than MKV.
Any other suggested options?
(And to rule out the obvious answers: Use a PC, just use the video without audio to edit)

[Mister Hatt]

Can't say I know this program you're using but I just transcode the content in avconv/ffmpeg or remux it to another FCP friendly container. The AVC should play fine as well as most audio formats. MKVtoolnix runs perfectly well in OSX so there is no reason not to write a wrapper script or just do it by hand. MKV isn't a codec so you can safely recontain your content without any conversion/encoding. I suggest reading one of the guides somewhere again for the difference in codecs/containers/formats and why you should know them.