Hi,
it's due to the way that Google Analytics manage domains for the API integration when changed as in your case.
Please refer to the FAQ
http://storejextensions.org/faq/why-the-google-analytics-integration-shows-stats-for-a-different-domain.html
at the bottom
QUOTE:
As a final recommendation when you register a Google Analytics property as http://www.mywebsite.com and you change it at a later time for example to http://mywebsite.com despite the fact that Google Analytics shows the new domain http://mywebsite.com in the admin console, it internally never changes the original domain that continue to be http://www.mywebsite.com. The original internal link will continue to be used even for the API integration with JSitemap that needs to be configured for http://www.mywebsite.com and not http://mywebsite.com. You have to delete and create again a new property in Google Analytics using http://mywebsite.com to have it really changed.
Cheers,
John