Domain Mapping plugin not working unless I remove sunrise.php

Domain Mapping plugin not working unless I remove Sunrise.php.

site = New blog created by network admin

When I remove sunrise.php I'm able to access my sites using example.com/sites and have access to everything which includes setting a domain in Domain Mapping plugin.
Obviously the domain mapped will just land to example.com as specified by the domains A record.

When I activate the sunrise.php I cannot access my sites because I'm redirected to example.com and as such I can't visit dashboards to map domains.

I have also tried to entering the domain straight into a site's url setting e.g http://www.domain.com and it works, BUT the major problem is I still can't access dashboards of the sites.
Help!