SharePoint - Data at the root level is invalid. Line 1 , Position 1

When you open a file with SharePoint Designer, it creates all kind of FrontPage Server Extension functionality in your web application. One thing it does it that it creates a _vti_cnf folder in every folder you have in your web application.
If you remove all these folders you fix your problem.
http://weblogs.asp.net/soever/archive/2008/01/29/edit-file-in-wss3-web-application-with-sharepoint-designer-blows-up-your-web-site.aspx