Hmm, as a test, I opened the Library window (Ctrl+Shift+b) and expanded Tags in the left column.

I found a tag called deadsites where I had put a non-working bookmark. When I deleted the bookmark using right-click > Delete, the tag was deleted, too.

Is that the area where you see tags that don't have any matching bookmarks, or do you see them somewhere else?

Thanks for your reply. Yes, the non-linked tags were in the expanded box on on the left side. I couldn't delete them, probably because they had no bookmarks associated with them.

I fixed this problem manually by first making a backup of the bookmarks, then deleting places.sqlite. The first time I tried it, it didn't fix the problem because the bookmarks were automatically restored from Firefox backups. I had to delete the automatic backups and places.sqlite, and that finally killed the unused tags. Then I restored the bookmarks from my backup and the problem seems to be fixed.

Oh, I was going to suggest trying to create a bookmark, tagging it, then removing the bookmark, but your method probably was more thorough.