If the issue is related to permalinks it probably has to do with your server configurations and not the theme or WordPress. Are you using nginx by any chance?
Try using priorities to add your post navigation and related posts. To make them appear below the meta utility try this code:
add_action( 'enlightenment_entry_footer', 'my_post_navigation', 12 ); add_action( 'enlightenment_entry_footer', 'my_related_posts', 12 );