are you talking about mediabox here ?

Its the same thing. They are also in /home/user/.mediabox/playlists directory.

eg. my movie name is "20100501_001"

-- cd /home/user/.mediabox/playlists
-- grep 20100501_001 *
it shows
Playlist.m3u:#EXTINF:-1,20100501_001
Playlist.m3u:file:///home/user/MyDocs/DCIM/20100501_001.mp4

So you have to delete these two entries from Playlist.m3u