When you ran Remove Deactivated Friends, it looked like it worked — but it wasn't actually unfriending anyone. Deactivated Facebook accounts don't appear in the friends search results, so the app silently moved on without doing anything.
In v2.1.2, the app now visits each deactivated friend's profile page directly and unfriends them from there — which always works. Your deactivated friends list will now clear properly when you hit Delete.