Pagination issue for Custom Post type in wordpress 3.0

[WIP-Themes]

Try this mate, use caller_get_posts and reset the wp query after looping

$args=array(
	'post_type' 		=> 'portfolio',
	'post_status'		=> 'publish',
	'orderby'                    => 'menu_order',
        'posts_per_page'         =>6
	'caller_get_posts'	        =>1,
	'paged'			=>$paged,
	);
query_posts($args);
while (have_posts()): the_post();

    //loop code here

endwhile;

//pagination code here

wp_reset_query();

hope this help,

good luck