Do you already have something installed on the root directory of your hosting? Web templates or anything? Fantastico won't install multiple tools in the root directory. If you have a website, foru, or any other application installed in your root directory, you will have to create a subdomain for use with WordPress like "yourdomain.com/blog" or "blog.yourdomain.com".
Not sure if you got this fixed yet but Fantastico places a file in the root of your web directory, I think it is called fantastico.txt to keep track of installs and versions. If you have nothing else installed by fantastico, you can rename this file and see if that fixes the issue. You could also download this file as a backup, delete the one in your root directory and that should correct it.