setting location of favorites and startup folder via registry file

I have made a reg file that is supposed to change the location of two folders. I execute the reg file, and I checked the registry and my changes are there. But when I start the computer, the programs in the old startup location run instead of the new location, and the IE favorites are also still from the old location. Is there something else that needs to be changed?

Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Shell Folders]

This is on a windows 7 computer.

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