Have you tried perfectTUNES from dbpoweramp? It works on folders or whole drives full for music. It has 3 modules: Album Art, DeDup,, and AccurateRip. The Album Art module analyzes your whole collection and then displays (and attempts to fix with your consent) albums without artwork or with low resolution artwork. DeDup analyzes for duplicate tracks (ie, you might both FLAC and mp3). AccurateRip analyzes and compares your files to the AccurateRip database. It can't fix problems, but can at least alert you.
