This is a known problem that I have fixed in the coming version of mctvc. The problem is, that the automatic language detection in some strange cases is unable to select the right stream. Only way to convert those files is to manually select the right stream.
For WTV files you can run the GUI of remuxTool (tools/remuxTool.jar) and select the audio you want. For other files you will have to create a custom commandline (ffmpeg) and use the map parameter to select the correct stream. If you want to go this way and need help, let me know and I can assist you. Thanks!
Creator of MC-TVConverter