I suspect that the "updatemedia" mechanism doesn't recognise them when scanning for new media, can you play them with xine on the KDE desktop?
The .mkv file type need to be added to the pluto_main -> MediaType table. The 0704 DB schema did not allow enough space to add additional file types. In 0710 the schema has been extended so there is additional space for more files types... and .mp4 & .mkv filest types have been added :-)
UpdateMedia will scan for all of the file types stored in pluto_main -> MediaType