WordPress version 4.4 changed the way the menu structure was returned when using a custom menu. The symptom is that a menu item before a menu with a submenu would show an indicator that there were child items, while the actual parent of the submenu would not show the indicator.
To fix this problem you can eithor (1) edit bfa_new_wp3_menus.php and change line 43 from
$newmenu = preg_replace("/<li (.*?)class=\"(.*?)\">(.*?)\n(.*?)<ul class=\"/i","<li \\1 class=\"rMenu-expand \\2\">\\3\n\\4<ul class=\"rMenu-ver ",$newmenu);
$newmenu = preg_replace("~menu-item-has-children~","rMenu-expand menu-item-has-children",$newmenu);
or (2) download the attached file, unzip it and replace bfa_new_wp3_menus.php with the fixed version.