Hi,
During the uninstall process Windows Installer removes all resources (files, registry entries etc.) that are registered in the MSI.
In order to install a registry entry that will not be removed during the uninstall process first you need to make sure that it is the only resource in it's component in the "Organization" page.
For this component you can set the "Permanent" option in the "Atributes" page which will make the component to remain on the target computer after the application has been uninstalled.
You can read more about this here:
http://www.advancedinstaller.com/user-g ... rties.html
Regards,
Cosmin