multisite upgrade from 2.9.2

Hello guys
I have a problem on the upgrade from wpmu 2.9.2 to 3.0.5
Following the guides, I’ve just to run the automatic update, update the htaccess file and update the blog network.
The update itself does not report any error.
But what I’ve found is whenever I create a new blog (site) wp says correctly site added, but the only thing updated is a main site db table. Any site-specific table is created.
Furthermore, on the admin page, the link I have as backend admin page is not the one I’m expecting but the main blog one
e.g
main site backend: http://blog.mainsite.org/wp-admin/
site created “newsite”
site backend page: http://blog.mainsite.org/wp-admin/
and I expect
http://blog.mainsite.org/newsite/wp-admin/

Do you have any suggestion for something I may double check looking for what’s wrong?

Thanks, Yuri
PS:
the
define(‘WP_ALLOW_REPAIR’, true);
has been already test without success.
it returns several lines like “wp_<blogid>_<tablename> is missing”