Finally I found the answer. Vista assumes that some files need protection and that the user is the only one to make a change, so it makes a copy under their document folder to keep the changes. If you need to copy the file you need to use Windows Explorer and click on the file your are trying to find. If it has a virtual copy a Compatability File button will appear. Push the Compatability File button for the highed file and the location of the virtual file will show in the address bar.
Location of UAC Virtualized Files
Virtualization is a great feature for allowing legacy applications to work under Vista without requiring explicit user permission, but can cause a problem for applications that actually require the ability to write to directories protected through virtualization. For example, an organization may have a utility application that can go through Program Files, find any .NET configuration file with a database connection string, and allow the user to change the connection string to a new value. A tool like this obviously needs to write to files in the real Program Files directory.
Link to an excellent article