I was trying to test the multisite setup on my installation and I came up against this issue. Previously while using MU I could install WP at http://my-url/wp-mu, then define individual blogs under this, like http://my-url/wp-mu/skywalker, http://my-url/wp-mu/kenobi etc.
On 3.0 b2 I have WP installed in the same manner, at http://my-url/wp-ms. However, when I try to add a site called "skywalker", it becomes my_url_wp_msskywalker. Is this a bug or is this something that I botched during my network setup?