Domain mapping to multi-site install domain

Hiya,

Successfully installed the domain mapping plugin. I was able to successfully map all of the root domains. I have 100 root domains and 500 subdomains off the roots. The problem is that my main multi-site install domain disappears, is unusable, and is redirected to one of the root domains, usually the first one I mapped.

How can I have access to my original multi-site install domain?
Thanks!