OK - this is an odd one and if I were to start again I may do things differently.
I have a WPMU installation at http://www.cncllpgroup.com. We have live clients on subdomain sites, everything is working 100% fine with those and I DON'T want to do a reinstall for obvious reasons.
As part of the environment, we are setting up a full-blown wp.com style 'sign up and buy one' environment using the domain http://www.sneexl.com
The issue I am having is that, having used our initial root domain site and renamed the site sneexl.com, then creating all the usual cname records etc, when you go to sneexl.com, rather than going to the root - which is essentially the cncllpgroup.com root, wp-signup kicks in and takes you to http://www.cncllpgroup.com/wp-signup.php?new=www.sneexl.com which is precisely what I don't want.
I can't use a .htaccess redirect because we use the wp-signup later in the process and obviously a full redirect would bounce people back to the home page each time which would be silly.
Happy to provide more information but hopefully there is enough here so you get the drift