UpdateMedia daemon keeps the id3 tags and the database in sync and for this is using the latest version of libid3 (3.8.3) (see newbielink:http://id3lib.sourceforge.net/ [nonactive]). However, tt seems that it doesn't support yet 2.4 tag version.
When pluto boots up, all the files are automatically (re)indexed. If you don't want this, the only solution for you will be to rename/delete /usr/pluto/bin/UpdateMedia, but doing this, the database and id3 tags won't be in sync anymore. Also, UpdateMedia daemon will be disabled. We'll consider in the future the possibility to tell UpdateMedia to sync only the database using id3 tags, but not viceversa.