Exclude category from loop not working

Don’t use query_posts(). Use pre_get_posts instead:

function wpse82745_filter_pre_get_posts( $query ) {
    // Only modify the main loop,
    // and only in the blog posts index
    if ( is_home() && $query->is_main_query() ) {
        $query->set( 'category__not_in', array( '13' ) );
    }
}
add_action( 'pre_get_post', 'wpse82745_filter_pre_get_posts' );

This callback will exclude category 13 from the main loop in the blog posts index.