Huh, that’s pretty odd. Can you please include verbose output? (From either or both of a beet import run or a beet write run would be helpful.)
Also, it looks like you have copying enabled in the importer (the default). So are you sure you’re looking at where the new location, where updated files are being copied to, rather than the old location, where they’re copied from (and left pristine)?
Finally, in your configuration, the importer section is delimited with import:, not importer:.