Might want to check your Apache(assuming youre using a Nix server) to make sure your ServerName in the httpd config is set to default to the
www.domain.com version and not the domain.com
Also - if you are using relative links instead of absolute links and you dont have a trailing / on your relative links, this will cause Apache to issue its own internal 301 to go to the domain.com/directory first and then the
www.domain.com/directory which unfortunately Google's bot is very good at following.
You can check this pretty easily using something like the free link checker from Xenu as they will report the 301 redirects your server is doing.
As mentioned above - 301s can fix the problem - but ONLY if you have your server set correctly (and there are a bunch of hosts that don't know how to setup a server for SE botting)
added- dont pay any attention to the thing about sandbox - there is no such thing