I noticed when I updated to the New Domain Mapping 220.127.116.11, it broke my subdomain link references in the Pages & Posts areas. So for instance if I had a sub-site http://test.mydomain.com and created a new page in that sub-site http://test.mydomain.com/demo/ when I look at the link reference in the admin below the Title is shows http://mydomain.com/demo and when I click on View Page it goes to http://mydomain.com/demo.
I had to quickly revert back to the older version of the Domain Mapping Plugin but I'm sure you could test it and get the same result.
WordPress - 4.1.1
Domain Mapping - 18.104.22.168