In a PAGE that uses a custom template, I observed the erroneous behavior commented below:

$my_query = new WP_Query('post_type=post&post_status=publish&posts_per_page=6');
while( $my_query->have_posts() )
{
    $my_query->the_post();

    if( function_exists('is_protected') && is_protected($post->ID) )
    {
      //is_protected() does not return true even for posts which ARE protected
    }
}

I traced the bug into template-interceptor_rs.php::is_restricted_rs(), which is returning "nothing" in the final catch-all else:

else
  return ( isset( $scoper->restricted_ids[$src_name][$id][$op_type] ) );

The is_restricted() / is_protected() template function should now work correctly with secondary queries in the updated Role Scoper Development Snapshot.