I have used this to resurrect the sound from about 20 mkv files and it appears to have worked flawlessly. It will also allow you to extract tracks in order to build whatever composite container you like to build/use. Here's a section from the "readme."
"What is MoKgVm2DVD? MoKgVm2DVD is an application that provides the tools needed to prepare .ogm and .mkv files for use in DivX enabled DVD players. Note, this application will not allow you to play these files in non-DivX certified DVD players. When you open either of these two types of video “container” files in MokgVm2DVD, you will be presented with a list of video, audio and subtitle tracks contained in the file. Sometimes there will be enough information for you to determine what each track represents. If not, you can select a video and an audio track (and optionally a subtitle track) to preview the tracks in an mplayer window. Once you’ve determined which tracks you are interested in, you can either convert the tracks into an .avi file, or you can extract the tracks individually to manipulate in your favorite video application. Go to http://www.emmgun.com/ for more detailed information, instructions and troubleshooting."
It's not free but is worth the small amount asked just to be able to do batch processing though.