Query not returning CPT posts

I had a similar problem and posted the solution here:

http://wordpress.org/support/topic/role-scoper-updating-query_posts

query_posts causes the main WP_Query to be discarded. That may or may not be the behavior you want. If no, you need to update WP_Query, then you could update your functions.php file to include a register filter that displays your content types as part of WP_Query (see code at URL above). If yes, you don’t care about WP_Query, then I ran my query_posts after have_posts with this code in my index.php file:

    query_posts(array('post_type' => array('post', 'article', 'document', 'faq', 'video')));