Ok….I got it.
Go into you hosting and navigate to wp-content/themes/flat-responsive/flat-responsive/templates/template_functions.php
Go to line 123 and you’ll see this:
<div class="flat_responsive_menus">
<div class="flat_responsive_menu"><!--Primary Navigation Starts Here -->
<?php wp_nav_menu( array( 'theme_location' => 'primary', 'container' => false, 'menu_class' => 'navmenu', 'fallback_cb' => wp_page_menu( array('menu_class' => 'navmenu'))) ); ?>
</div>
Change it to:
<div class="flat_responsive_menus">
<div class="flat_responsive_menu"><!--Primary Navigation Starts Here -->
<?php wp_nav_menu( array( 'theme_location' => 'primary', 'container' => false, 'menu_class' => 'navmenu', 'fallback_cb' => false ) ); ?>
</div>
Then you can use your custom menu again. All we did was take the fallback_cb to false. And on mobile you have only the mobile menu again.
Thanks for the idea. Let me know if you got this taken care of so I can mark it resolved.