Programs that try to write data or configuration changes to program files instead of Users\username\AppData\Roaming will not be allowed to and will be virtualized. If you wanted to backup setting or data from a program that is being virtualized you would need to backup the virtual files as the exact same copies in program files will not be allowed to update. This also applies to programs that try to write to changes to HKEY_LOCAL_MACHINE\SOFTWARE. They are redirected to HKEY_CURRENT_USER\Software\Classes\VirtualStore. If you wanted to backup registry entries for your program and it has been virtualized you would want to backup virtualstore keys as the same keys at HKEY_LOCAL_MACHINE\SOFTWARE will remain unchanged since you installed the program. To see if your program is being virtualized you can go into the programs folder in program files and if it is being virtualized you will see a button at the top that says compatibility files (see attached). You can also go to drive:\Users\Username\AppData\Local\VirtualStore\Program Files. Appdata is hidden so you will need to unhide hidden folders in folder options to see it. More info about some issues with virtualization can be found in KB927387. I had scenario 2 problem discussed in the KB where I had unzipped files to a folder in program files but they were not there when I went to find them. I finally found they had been magically redirected to virtualstore. One way around files being virtualized is to check the box on your shortcut to run this program as an administrator. However, then you may get prompted whenever you try to open that program.