Why is the Windows Installer service leave behind files during uninstall?
Below is a listing of common causes of files being left behind after uninstall of the MSI .
Shared DLL: If you include the registry key: HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\SharedDLLs in an installation, it can reset the values of shared files on the machine and cause the DLL counter to not decrement properly when the MSI is uninstalled. Do not include this value in a .MSI.
Leave Installed on Uninstall: On the Components tab in Setup Editor, view the details of a component to view the 'Leave installed on uninstall' checkbox. If this checkbox is checked on any component, the component will remain on the machine following an uninstall.
Windows File Protection: If a file that you are installing is included in the Windows File Protection list, the file will not be uninstalled by Windows Installer. An entire component will not be uninstalled, if the key path of the component is a Windows Protected File.
For more information regarding this issue please view the article, "Removing Stranded Files", in the Microsoft Windows Installer SDK.
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