Before doing a rescan, do Tools/Advanced/Compress Library. When that finishes, restart MB and then rescan all files. Results?
If you exit MusicBee and delete the files "MusicBeeLibrary.mbl" and "MusicBeeLibrary.bak" in the Library folder, all information about your file paths, names, and tags will be gone. This would purge ALL your files info though, not just problem ones, and require that you let MB create a new library on its next start. Which might be the best thing actually.