First of all; great site, great service. I'm glad to be a part of this community here!
I recently started using your domain mapping plugin and just today I realized that the main site on my reseller account was also resolving to the site where I'm using wpmu and the plugin.
Let me explain. I have a reseller account under which I host many wordpress sites each having their own cpanels (no subdomain or add on hostings). I set up wpmu on one of those sites, got the dedicated ip, installed your plugin, added A records to two sites at the registrar for testing and it all worked fine at first shot. However, an hour ago I found out that the main site for my reseller account was resolving to the wpmu site although no domain mapping was done and no A record changes were made. For your info, when the address is typed in the browser, it redirects to the wpmu site sign up page with the site name added to the url as a parameter. This is no big deal as I can simply host the root site under the wpmu site as well and all will be fixed. So this is more out of curiosity..I suspect it has to do with the domain mapping code (no finger pointing, just a note).
If anyone has any ideas why this may be happening, please let me know.