I’m having a similar issue working with the BuddyBoss child theme. With the plugin activated, the name of my custom menu appears with no menu items in the drop down. The top tier menu items in the custom menu appear as separate menu buttons, and correctly have sub-pages where assigned. But there’s a dead menu link in the admin bar with the custom menu name.
If I build a custom menu with only one tier of menu items, all appears as separate menu items (no in drop down format) alongside the dead menu link with the custom menu name.