i had some issues in the past with miniDLNA indexing when i was using for example:
list media_dir 'V,/mnt/raid/Media/Movies' together with RootContainer=standard, when i switched to “browser” container and redefined all list-media-dir to not use V/P/A attribute(with service restart), all went fine. Also try it first just with one folder first and add next later on , one-by-one and each time test it.
i assume you have rights and ownership correctly set, so minidlna actually can parse the subfolders/files 
>> if the mount is actually shared samba folder and files were uploaded using smb protocol you might have strange chmod/chown on files/folders preventing minidlna to access them.
there is also this thread: miniDLNA not refreshing