Stupid me...
Yesterday after uploading some more files to my system the players did not see them though minidlna, too. Since this files have been mostly avi ones, the problem has to be some more general and not only related to mkv.
So, thinking about the problem I got struck by the lightning of epiphany: Permissions!
I uploaded my files by ftp in the public samba folder. Its owned by user nobody, and samba maps the guest account to this user. After ftp uploading (because samba gives me only 20 MB/s, while ftp is about 80-100 MB/s) I changed the owner by cli to nobody and thought this would be fine, but forgot about checking the read permissions - the files are marked for owner access only (700).
So, accessing the files through samba worked fine, because samba maps the user to nobody and is therefore able to read the files. Minidlna is not mapping permissions nor running as user nobody - so it was simply not able to read the files.
Because I uploaded the earlier files by samba, they had different permissions and minidlna could read them. The newer mkv files were upload by ftp, and so I thought the problem was caused by the mkv container.
Well, a 'chmod -R +r <path>' later everything works like a charm
Thanks to everyone for the help!
