Today, I was unable to convert an mkv video file to mp4 with audio intact. Every time I attempted to convert this file, I would receive an mp4 with excellent video playback, but no sound.
After doing my Googles, I came across this forum, and solved my issue by changing the audio file sample rate format to 48000 hz by clicking on the customize tab. And changing the codecs to MPEG 4 (AAC).
I hope this works for you as well.