Two Navigation Menus – secondary nav is including main nav

In your theme’s functions.php did you register a new WP Menu ?
by using a code like this:

register_nav_menus( array(
        'secondary' => __( 'Secondary Navigation', 'twentyten' ),
    ) );

And after that in your theme’s header.php under <div id="access" role="navigation"> you should add

<?php wp_nav_menu( array( 'container_class' => 'menu-header-secondary', 'theme_location' => 'secondary' ) ); ?>