Single VOB file to MKV?

[Romansh]

Have you tried using TSMuxer?

http://www.videohelp.com/tools/tsMuxeR

To create an MKV file?

[MiKeeVid]

MakeMKV might not be the right tool for the job. Perhaps mkvtoolnix would be better?

This is an old thread, but it has a high Google search result, so I'm adding some updated information. MKVToolNix GUI is the best software for converting a VOB container to an MKV container. It retains the original video, audio, and subtitles.
https://mkvtoolnix.download/downloads.html