[Sealy]

I had a similar problem and it turned out that google webmaster tools has an interesting 'feature'.

When you register a domain, say for example: http://www.cnn.com

Does not necessarily register if you have forced your server to use http://cnn.com (without the www. before the domain name).

If you have set up your web server like that, make sure you add the non www. domain to webmaster tools as well. For some strange reason, it seems some subdomains alongside certain settings in the webmaster tools area, will tell google that the two sites are totally different.