Background: Installed Win2008 + IIS7 + PHP 5.3 using the FastCGI method (used the Windows installer to configure IIS7).

Symptoms: PHP worked fine in my Default Site but when attempting to execute any scripts in Virtual Sites or Virtual Directories, every single PHP file would yield a 404 error message.

Solution: The problem ended up being that the ‘open_basedir’ config variable from the php config file is applied to ANYWHERE that PHP is run…regardless of what the actual home folder should be for a site (PHP picks up the basedir during installation and statically enters it in your php.ini file). The default ‘basedir’ will be whatever the root of your ‘Default Web Site’ in IIS is (usually c:\inetpub\wwwroot\). If you comment out this line (enter a semicolon before the line) and restart IIS, it will solve the problem. If you’re running PHP as a FastCGI module, you’ll actually have to rename (or copy) the php.ini file to a file named ‘php-cgi-fcgi.ini’ in the same folder as your php-cgi.exe executable. Be sure to restart IIS!