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I am setting my navigation menu up using the following snippet in my functions.php.

add_action( 'init', 'add_menus' );
        function add_menus() {

                register_nav_menus(
                    array(
                        'main_nav' => 'Main Navigation',
                        )
                    );

$new_menu_id = wp_create_nav_menu( 'Navigation' );                  
$menu1 = array('menu-item-title' => 'Home','menu-item-object' => 'page','menu-item-object-id' => get_page_by_path('home')->ID,'menu-item-type' =>     'post_type','menu-item-status' => 'publish');         
$menu2 = array('menu-item-title' => 'Register','menu-item-object' => 'page','menu-item-object-id' => get_page_by_path('register')->ID,'menu-item-type'     => 'post_type','menu-item-status' => 'publish');         
$menu3 = array('menu-item-title' => 'Login','menu-item-object' => 'page','menu-item-object-id' => get_page_by_path('login')->ID,'menu-item-type' =>     'post_type','menu-item-status' => 'publish');

// add a menu item to that new menu
wp_update_nav_menu_item( $new_menu_id, 0, $menu1 );
wp_update_nav_menu_item( $new_menu_id, 0, $menu2 );
wp_update_nav_menu_item( $new_menu_id, 0, $menu3 );

// set our new MENU up at our theme's nav menu location
set_theme_mod( 'nav_menu_locations' , array('main_nav' => $new_menu_id ) );
}

When I create a new multi-site it generates the menu and the menu items, however it does not assign the Theme Location as set by:

set_theme_mod( 'nav_menu_locations' , array('main_nav' => $new_menu_id ) );

If I delete the menu and then refresh it does then assign it correctly, any idea what is going on?

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