Nginx & Magento CE 1.9.0.1
I created an additional store in a sub-directory (e.g. shoes.com/sneakers/). Every link in the main site - shoes.com - works. If I try to visit a CMS page of the shoes.com/sneakers/ site (e.g. privacy), I get a 404 from the main site - shoes.com. If I precede the URL of the CMS with index.php so that the entire URL looks something like shoes.com/sneakers/index.php/privacy it works however the Nginx configuration I'm using now is using and hiding the index.php in the URL for anything at shoes.com.
Is it possible that sub-directories are excluded from this directive or that through misconfiguration, it only applies to the main site?
Additional Information: I followed Magento's documentation to create a secondary store - copying index.php and .htacccess over, changing the $mageRunCode in index.php and creating symbolic links for the necessary folders. This is working locally on my MAMP environment but not on staging. I checked permissions and still no luck. It's loading Magento, the correct package but not the correct theme which I have double-checked in the admin panel.