Yes, I'm referring to Main.dwt.php.
It just screws up the formatting of the page. By adding admin.css and home.css files in the head (as it does by default for some strange reason) - those files have tags that override the tags that are in content.css which are made for the main template pages. So once you remove those calls to admin and home css files - your pages will look similar to the pre-made pages (such as privacy_policy.php, and/or termofservice.php). That's assuming that you are creating the new pages similar to those pages (ie. using the div class contentBox).
It's just about the page format (where it places the background image for the main content - it's different when you have home.css in your head portion of the template). At least, it was for me.
Hope that helps.