Magento backend not working with index.php in url

[santerref]

Hello,

Recently I have upgraded my Magento from 1.9.0.0 to 1.9.1.0 and now the backend return a 404 error...

I have a "complex" structure for my website and I think the problem is related to my .htaccess.

Currently, to solve the problem, I have created a duplicate of app/code/local/Mage/Core/Model/Store.php and removed all index.php in URL.

The problem is that I can't use Magento Connect because it always ask me to login when I try to update, install or remove a module.

Suppose my website is http://example.com/

I have a magento running on http://example.com/ and a wordpress running on http://example.com/my-wordpress

My www-data structure is like this :

www-data/.htaccess (http://example.com point here and I use the .htacccess to redirect request to the good directory

www-data/magento 

www-data/wordpress

www-data/magento/.htaccess

www-data/wordpress/.htaccess

[santerref · Accepted solution]

Problem solved by adding 

$_SERVER['SCRIPT_NAME'] = '/index.php';

In index.php

Thanks to http://husseycoding.blogspot.ca/2013/01/installing-magento-in-subdirectory.html