Nathan

I was able to solve the problem by adding a check to see if the query_vars contains post_type.

    
public function wp_es_pre_get_posts($query) {
    if (!empty($query->is_search) && !$this->is_bbPress_search()) {
        if (!isset($query->query_vars['post_type']) && !empty($this->WP_ES_settings['post_types'])) {

Here is a way I came up by just changing ur custom error page and then adding a part of code to WordPress.

https://www.nathanm.com/2006/07/02/wordpress-permalinks-removing-indexphp-in-iis.html

Try this..
https://www.nathanm.com/2006/07/02/wordpress-permalinks-removing-indexphp-in-iis.html