@George
I found that this plugin is working based on table "wp_domain_mapping". Redirection loop will happen or register page will display if the requested domain is not found in this table.
Plugin it is not allowing to create entry with blog_id =1. I have disabled this validation and created an entry, then it works, that is I can able to map main domain as well(but hosted in different servers). But I am not sure what all the consequence can happen due to this practice.