No problem. The query is built dinamically respecting the options you choose on the backend. The file you are looking for is the plugins/ajax-search-pro/includes/search_content.class.php. The significant lines are 186-230. You will see a part of a huge query there.
What I think you should try first is to eleminate the non-published posts from not being searched. I still think the problem is related to that. So, try to edit the line 220:
($wpdb->posts.post_status='publish' $searchin) AND
($wpdb->posts.post_status='publish' OR 1) AND
Save the file, refresh your browser on the frontend and do a search. I'm almost sure, that you will see results from the custom post type 🙂Best,
If you like my products, don't forget to rate them on codecanyon :)