The script is complete when the Command Prompt window closes. In other words,
once it has finished adding the m3u playlists to iTunes, it's done.
It cannot affect iTunes after it completes, because it isn't running. Nor does
it change any iTunes settings. I suppose it's possible that iTunes modifies the
playlist files, but I doubt it.
I think your problem is iTunes. If you add a folder, it automatically adds both
song files and playlist files. It has always done this, as far as I know.
--
Rob