Microsoft has released a fix-it to help restore personal files after you perform a custom installation of Windows Vista or of Windows 7.
"In some scenarios, you may be unable to perform an upgrade from an earlier version of Windows. If you cannot upgrade, you may have to perform a custom installation. When you perform a custom installation of Windows Vista or of Windows 7, Windows creates a Windows.old folder that contains the files from your previous system.
You may want to recover your personal files from the Windows.old folder, and move them to the custom installation of Windows," explains Microsoft in KB932912.
To fix this problem automatically, click this "Fix it". In the File Download dialog box, click Run, and follow the steps in the Fix it Wizard.