It might be two things. First, if you don't have some or all of the extra gstreamer codecs installed, I'm not sure the mediaplayer will recognize certain files. Second, the mediaplayer is not that flexible about mime types. For instance, I'm running the mediatomb UPnP server and it's default export mime type for ogg-vorbis files is something like:

application/vorbis+ogg

I had to change it to:

audio/vorbis+ogg

before the files would be recognized by mediaplayer. The file manager is more flexible. See if you can see some of those invisible media server files with it. If so, you might have one or both of the problems I described.