plugin makes my nav menu disappear

Can you provide a url? You sure you are not using a different plugin which suppose to do the same as the post types order? As there is no connection between this and the menu

the url is : https://deepfry.wpconsult.net/
there are 2 links (home,projects) generated by code :

// Filter wp_nav_menu() to add additional links and other output
function wpc_nav_menu_items($items) {
	$homelink = '<li class="home"><a href="' . home_url( '/' ) . '">' . __('Home') . '</a></li>';
	$newestprojectlink = '<li class="projects"><a href="' . wpc_get_latest_project_url() . '">' . __('Projects') . '</a></li>';
	$items = $homelink . $newestprojectlink . $items;
	return $items;
}

and the rest are from a WP 3 nav menu.
when I activate the plugin, the menu items aren’t being created

Have you been able to solve this problem? I am having the same issue. As soon as I activate the plugin, my main nav menu disappears: https://www.amplify.lt/alita2/category/produktai/brendis/

This should be already fixed. Can you please contact us with a login to your blog?

As an FYI, I had the same issue – using Genesis/Agent Press 2.0 with the dsIDXpress plugin, the nav menu disappears on any of the pages generated with the IDX plugin. When I disabled the post order plugin the issue disappeared. Hope this helps with the troubleshooting.