I have some m3u playlists whose entries are of the form ../music/[whatever file]. When I play from these playlists, amarok says "This file is not in your Collection!" because it does not understand that ogg/../music/[whatever file] (the path that it gets from the m3u) and music/[whatever file] (the entry in amarok's database) are equivalent. A similar problem occurs with symlinks.
Please report this upstream. Anyway they are already working a solution for this kind of problems, by using ATF.