Very interesting, I have no clue whatsoever why is it happening. Could be some sort of a weird bug somewhere, but the plugin requests the terms from WordPress internally in the first place, so it may actually be something in the WP core.
The back-end redesign is going slowly but surely. Recently the search cache and the search statistics interfaces were rebuilt. Next comes the rest of the menus and finally a completely new search configuration interface – in fact it is going to be separated to 3 different “template” areas, one for the search bar, one for the filters and one for the results – and each different search/filter/result configurations can be paired with each other.
It is still a long way to go though, no estimate at this time.