problems exluding categories

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

function wpse65927_filter_pre_get_posts( $query ) {
    // If this is the blog posts index,
    // and if this is the main query,
    // exclude category 6
    if ( $query->is_home() && $query->is_main_query() ) {
        $query->set( 'cat', '-6' );
    }
}
add_action( 'pre_get_posts', 'wpse65927_filter_pre_get_posts' );

Put the above hook and callback in functions.php. Don’t modify any of your template files, including index.php or home.php, at all.