In the past I had used the plugin to assign "Genre" to just over 400 books and "sub-genres" to more or less one thousand books. Since I'm a data-hoarder that information is still in my database and the books are a broad mix of genres.
When the previous plugin worked and I flagged only Genre, I would get only one tag and that was perfect for my needs - I was quite more interested on assigning genre and sub-genre to my books than on Tags
. Now, flagging only Genre, I get a mix, including sub-genres, age level, time period.
Is this what you expected?