They are indexed with mt-daapd and are in the Web Interface’s Playlist.html library.
That’s kind of strange. If they show up in the playlist.html, then they have to be sent to the client. Is it possible that it isn’t indexing the metadata right and that they files are actually *there*, but they show up with different/wrong metadata? Like, maybe they show up with a title of the filename, rather than song title, or something like that.
If it shows up in the playlist.html, then it’s getting sent to iTunes. Those lists are populated the same way, using the same mechanism. If the playlist gets those files, so does iTunes.
Now, if it’s missing from both, then it’s likely a permissions problem — the “runas” user can’t read the files (or doesn’t have r-x permissions to a directory above the file in question).