Ok, I found the problem.

When adding the index.php file to the following dirs my site would forward to the root of my web server.

admin\includes\extra_configures

and

includes\functions\extra_functions

So I didn't put the files there!

I really like the way these files work, however, since they are php access is not granted to them (due to some .htaccess files). I would like to keep the .htaccess files there (for obvious security reasons), but is there a way I can bypass the restriction on .php files for inde.php only?