Cool, so to replicate (if you can't link the site) the problem we need to have the HTML output of this:
<nav id="site-navigation" class="navigation main-navigation" role="navigation">
<a class="screen-reader-text skip-link" href="#content" title="<?php esc_attr_e( 'Skip to content', 'twentythirteen' ); ?>"><?php _e( 'Skip to content', 'twentythirteen' ); ?></a>
<?php wp_nav_menu( array( 'theme_location' => 'primary', 'menu_class' => 'nav-menu' ) ); ?>
<h3 class="menu-toggle"><?php wp_nav_menu( array( 'theme_location' => 'small-screen-nav-menu', 'menu_class' => 'nav-menu' ) ); _e('Menu'); ?> </h3>
</nav>
</header>
<section id="tab_links">
<?php wp_nav_menu( array( 'theme_location' => 'tab-nav-links' ) ); ?>
</section><!--end of tab links-->