I assume you're talking about the Tweaker? That's the program you downloaded from Arks-Layer, the website. It appears the Tweaker is updating the game fine, the issue you're having is GameGuard (the horrible
cheat protection the game has) acting up. Try Troubleshooting -> Fix Gameguard Errors.
Also, there's a thread on http://pso-world.com
where you can post issues and get help. I'd suggest posting this sort of thing there, since this site is mainly for the english patch and such things.