I am able to setup multisites with WP 3.4.2 without any problems. In fact I have done so, many times, using subdirectories. So the WP installation is in a directory and not on the root.
Following all the steps and the same intructions, I cannot make a working multisite installation with WP 3.5 beta 3. I get to the point where all is setup, I can create sites, but when trying to view them or get to their dashboard with my superadmin credentials, I get permission errors. I am really baffled. I also realized that during the setup WP 3.5 does not make me to create the blogs.dir folder. Even if I create it anyways, it does not work. Ant help will be greatly appreciated, than you in advance.