I think I found a problem with Custom Post Type Permalinks.
Both plugins use flush_rewrite_rules() function and when they are active, FL Top Level Categories go last and flush rules. When the line add_action('init', 'fv_top_level_categories_permastruct'); is removed – everything works right.
I have the same problem, but with Custom Post Type Permalinks plugin. When create or edit category all their rules not working.
