Only wanted to order one taxonomy, overrode multiple

Seems to be no way to select which taxonomies are or aren’t sorted by this plugin. I only ever selected a single CPT’s taxonomy, set its order, then hit update. And this overrode sorting for other taxonomies on the same CPT. Deactiviating plugin restored the order. If the admin interface had a clear UI to add (and remove) custom sorting then I would have given 5 stars.