The reason this is happening is because the mkv container has either multiple or a single unsupported audio track (usually 5.1 AC3 encoded audio). This is common issue with extremely high-quality MKV rips. Audio transcoding is generally a huge pain to do, however I do have a somewhat simple fix for you (and anyone else looking at this, for that matter).
The solution:
https://drive.google.com/open?id=0B_TJ7NPe0Rood29NWmVpdHBUZHM
This link will lead you to a download of a program called XenonMKV. What it will do is demux your MKV file, reencode the AC3 into stereo AAC (a more widely supported format) and repackage everything as an MP4 file. This conversion will be completely lossless. The settings should be pre-configured right out of the box, but on the offchance they're not, they should be the following:
Files and folders: Don't split files, even if they are over 4GiB, {you should choose a location for the temp files, preferably somewhere with at least 10-20 GB available at all times}, Warn me about these files but continue to process them.
Tracks: Everything disabled
AC3 Decoder: When coverting audio, normalize to +0dB checked, dynamic range compression light, next two unchecked, stereo downmix mode dplii
Nero AAC: Target Quality mode 1
Last Steps: Use 0.4.4, stable fallback
mp4box should output to my scratch folder, then move the finished product (it's safer that way, you don't want to be building an mp4 file on a flash drive)
last two unchecked.
And there you go, buddy. It should work great. If you have any further audio issues (audio too loud, too quiet, or too dynamic), try playing around with the AC3 decoder settings until you find something that works for you.
PM me if you have any further problems.
Best of luck!