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Why are some folders, map documents, and template files visible through ArcMap but not when browsing through Windows Explorer on Vista?
Folders, map documents, and templates saved to locations under C:\Program Files, for example, a personal map template folder in C:\Program Files\ArcGIS\bin\templates, are visible in ArcMap but are not when browsing Windows Explorer on Vista.
This is because the user profile is a member of the Users group, which does not have write access to the Program Files directory. Vista automatically redirects the file/folder to the virtual store, a location in the user's profile, for example C:\Users\<your_user_profile>\AppData\Local\VirtualStore\Program Files\.
See the Data Redirection subsection of the Microsoft TechNet article linked in the Related Information section below for more information.