When using multiple post types (such as standard posts mixed with custom posts), it may become necessary to query several types at once. Note that whenever you query posts, you need to ensure that pagination is enabled as well. You may do so by using the following code:

<?php
    // enable pagination using the $paged variable
    $paged = (get_query_var('paged')) ? get_query_var('paged') : 1;

    // query posts
	query_posts(array(
		'post_type' => array(
			'post', 
			'custom_post_type',
			'another_custom_post_type'
		), 
		'paged' => $paged )
	);
?>

Replace the custom post types in the query_posts array with your own.