I dont follow, are you saying that you get errors when running the checkout wizard?
or that the after the pages are created, these files are missing from the site?
if you are getting errors when running the checkout wizard, uninstall eCart from the extension manager, open DW and a php page to trigger the WA installer to uninstall the files.
then reinstall eCart, make sure to download the latest version, 6.0.3 and reinstall it.
open DW and a php page to start the WA Installer again, make sure to restart DW after the installer completes.