I'm using Microsoft's Azure hosting (so Windows not Linux)and I'm having trouble with the Multisite installation. I've installed WordPress 3.5.1 (using the Azure wizard) and this worked fine and as expected. Then I added in the Multisite code, setup my network to use subfolders (subdirectories), and followed the instructions to modify the web.config and wp-config files. Finally, I created my additional network sites through the "Add New Site" interface. I can access all of the subdirectory sites. However, I can't get to the wp-admin dashboard of any of the new sites. In other words, I can access mydomain.azurewebsites.net/example but not mydomain.azurewebsites.net/example/wp-admin. When I try, I get "The resource you are looking for has been removed, had its name changed, or is temporarily unavailable." (Or basically a 404 error).
I followed these instructions: http://www.windowsazure.com/en-us/develop/php/tutorials/convert-wordpress-site-to-multisite/ and tried searching, but can't figure it out.