Ah, there's the rub. While the VFP 5/6 SETUP wizard allows you to provide a "Post Setup Executable", there is no way to specify a "Post Ininstall Executable". This is one of the reasons NO VFP 5/6 application that used the setup wizard could be Certified my MS as "approved". The specs require that other than a possible temp file / directory, a Certified app must completely reverse an install on the total uninstall option.
With an uninstall you'll have to provide a "manual" procedure to remove leftovers from the desktop, or in a re-install you'll need to add "smart" code in your "Post Setup Executable" to look for and remove any old install components.
Of course upgrading to a "real" installer could eliminate the problems in the future.
Rick