In the first place its not an issue and doesnt need to be fixed - its supposed to be different - idiot - the only thing that may have been fixed for you is that your server admin figured out how to run Apache correctly.
The only fix Google has ever done for anything to do with the differences between
www.domain and domain was the tool they added to WM tools to set your preference for which got listed and botted - the PR (displayed in the toolbar I assume) was not and still is not an issue as it should be different - again dependant on your server config file(what the attribute servername is set to)