New Addon Domain Showing Up Wrong

I just added a addon domain in Cpanel at hostgator & the

domain is also showing up at the end of my primary domain
like this

http://widgets.com/ (Primary)

http://widgets.com/newaddondomain (Addon sub folder)

This should create a duplicate content penalty with
Google and get me sanded boxed.

It shows up as a folder because google finds the folder
under your primary domain.



The only way to stop that site to show up as a folder would be put a robots.txt file in there but then that would not help because it will keep the addon domain from being stored in google also.



How do I get the domain not show up under the primary as a sub folder.