My guess is, somehow the id3 module can't read the tags from your files, that's why it's falling back to the old guess-by-filename scheme. Not sure why, though. Do you know if your tags are id3 v1, v2, or both? You could try falling back to id3v1 and see if it helps.

Tip: After changing tags for existing files, you'll need to run "full scans" since information for that file already exists in the database. While testing, this will take long and be boring. Instead, upload/copy your tag-edited file as something else (rename it), then run a regular scan. This way scanner will detect the new file and read the tag.

As for the koalas, try disabling "heuristic cover art search" from scanner, and running a "full scan". A full scan also instructs the scanner to re-download existing cover art (if there's any available) while a regular scan will only try downloading the non-existing art.