This particular movie .mkv has 2-audio streams. The 1st one in the list (MC26) is the non-English audio stream, the 2nd one is the English stream. When you go to do the convert format, the options for audio is empty whereas the Video has options. It looks like convert format selects the 1st audio stream as opposed to following MC26 Options>Video>Subtitles & Languages selection (as it does when it plays and hence why it seems to be correct. Player>Display Options>Streams. There is a V:Eng video and A:ac3 and A:DTS. The ac3 is the non-English and the DTS is the English.)
It seems like the convert format has no means to select the audio stream to convert with the video.
The converted .mp4 file has no audio stream selections available and hence the non-English version.
Hope this helps.
PS: as the kids wanted to watch this on the TV along with others, I setup and used the Media Network and via a browser on the TV we were able to surf over to my MAC, connect with JRiver and play the movie(s). Pretty slick
Gotta just love MC26!!