I don't know that this explains any of your incorrect results, but it sounds as if you have songs from "greatest hits" albums marked as being "part of a compilation". There isn't any official definition of what the "Part of a compilation" setting really means, but iTunes' automatic file organization implies that this setting should be used on songs which belong to an album comprised of different artists. I would be interested in hearing users' experience in this regard, either here or on the LairWare forums.