If you already made sure that every emails was correctly published via "Hikashop->System->Emails", note that Hikashop uses the standard joomla email sending functions. If you have a problem only on ONE email, it means that the problem is the content of the email.
What you should try also is to send an email via the interface in sales when changing an order information. Does that work ? If yes, then, the problem is really the content of the order creation notification.
It could also be that your hosting company doesn't allow you to send more than one email per thread and at the end of the checkout, two emails are sent (1 to the customer and 1 to the vendor). So you might want to check on that with your hosting company.