Since updating the server, I cannot add neither Movies nor TV Shows to plex (in mkv format). The naming of the files is correct, as it is the same name format of the rest of my files that the server can still read. When I display by folders, I can see there the newly created folders, but no .mkv files show up in there.
That very odd as I only use mkv and have not seen anything like your describing. I would try doing the Plex dance and see if will appear. I use new scanner, maybe that the differece.