Custom Post Type Taxonomy Permalinks

I am having a very specific issue on permalinks.
I have a custom post type and a taxonomy.
Using the function below sorted out the correct structure of the taxonomy permalinks.

function phototype_permalink($permalink, $post_id, $leavename){
    if (get_option('permalink_structure') != ''){
        $post = get_post($post_id);
        $rewritecode = array(
            '%postname%'
        );
        if (strpos($permalink, '%postname%') !== FALSE){
            $terms = wp_get_object_terms($post->ID, 'phototype');
            if (!is_wp_error($terms) && !empty($terms) && is_object($terms[0])) $phototype = $terms[0]->slug;
            else $phototype = '';
        }
        $rewritereplace = array(
            $phototype
        );
        $permalink = str_replace($rewritecode, $rewritereplace, $permalink);
    }
    return $permalink;
}

add_filter('post_type_link', 'phototype_permalink', 1, 3);

then adding to args this:

'rewrite' => array('slug' => '%postname%'),

Regular posts also fit themselves to the new structure.
However I am getting 404 error on pages. The wierdest thing is that I am not getting this error on pages with parents.

For ex: I am getting 404 error here: domain.com/products-page/
and here not: domain.com/products-page/your-account/

Any idea?