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Hi,
Many thanks for your feedback. There are a number of points to make, I think.
Firstly, the "Copy To/Set As Default Profile" functionality in User Profile Manager was originally added to User Profile Manager just in order to replicate the "Copy To" functionality available using the “User Profiles" dialog box on Windows XP. (We had to replicate this functionality because User Profile Manager replaces the “User Profiles" dialog box.) This it does. The "Copy To" functionality in XP does not fix all the paths in the registry and neither does User Profile Manager. (May be this is one of the reasons why Microsoft dropped the "Copy To" functionality in Windows 7.)
You say that the paths in registry that point to the source profile exist throughout the registry. This is true, but the vast majority of these paths relate to user specific data like Most Recently Used file lists. If you are creating a new default profile, it is best practice to strip the source profile of as much of this data as possible – or not create it in the first place. The default value for the HKCU\Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders registry key is !Do not use this registry key 
Importantly, what’s the problem? Does having these paths in the registry actually cause an issue? The feedback we have had indicates that they don’t. May be that’s not the case in your environment; if so, let us know what you are seeing.
Finally, if the only thing you are using User Profile Manager for is setting a default profile, you should not be using User Profile Manager. Please use our free http://www.forensit.com/support-downloads.html - DefProf utility instead. More on that http://forensit.blogspot.com/2010/09/changing-default-profile-on-windows-7.html - here .
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