I recently repeatedly experienced duplicates in iTunes after importing directories of mp3 files. Almost all files (but not all) would be visible twice in iTunes and they would also exist as two distinct files in the iTunes library, but the files would be identical. Some files even would be visible three times.
I now found what is the cause: An m3u playlist in the directory will cause all the file in that playlist to be impoted and in addition all mp3 files in that directory are also imported, hence all files in the m3u list will appear twice.
The solution is to erase all m3u files (or all non-mp3 files) before importing directory structures.