Menu Location's don't appear

I’ve come across a strange bug. I copied a custom theme that I based off of bones to a new install. The registered menu locations don’t appear in the Menu area of the admin panel. I know they are registered because they are logged correctly with get_registered_nav_menus(). I am calling wp_nav_menu() with the correct location slug. If I pass a menu name into wp_nav_menu() it is output correctly. If I only list the location, it is using the listed fallback. Anyone have an idea what might be causing this?