I recently created a new wordpress 3.5.1 install with the intention of enabling multisite. I followed all the official instructions and everything seemed to be working until I got to actually creating a second site in the network with a subdirectory.
I created the site (ex: named 'blah'), but when I tried to go to domain.com/blah or domain.com/blah/wp-admin, it was like I was looking at the main site in the network.
I tried many different recommended .htaccess variations, checked every gotcha that official wordpress documentation, the wordpress stackexchange, and other wordpress blogs mentioned, to no avail.
Finally it took some help from my life pair Jake Goulding to spot that in the site info for the subsite, I had '/blah' for the path setting, and since the main site had '/' as the path, perhaps it should be '/blah/'.
Adding the trailing slash in the path for the site allowed wordpress to recognize it and going to domain.com/blah/wp-admin immediately started working.
I admittedly am not very experienced with wordpress, so perhaps this is something everyone else was able to figure out, especially since I didn't see anyone else recommending that you check this.
But I found the help text in the Add a Site form to be misleading:
It says "Only lowercase letters (a-z) and numbers are allowed." To me, that says "You should not enter a trailing slash", when in fact the behavior I see is that you MUST enter a trailing slash. Either the help text should be changed or, even better, this should work whether you enter a trailing slash or not.