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nginx, ispconfig & codeigniter - remove index.php


I am developing local with Apache with mod_rewrite. But my live server runs nginx with ispconfig. I'm having a hard time making my website work.

The first part works, I can access the site and it works (www.DOMAIN.com/SUBDOMAIN). But as soon as I want to access a controller it shows a 404.

I changed base_url after uploading it. I modified uri_protocol aswel
$config['uri_protocol'] = 'REQUEST_URI';

Is anyone with experience with nginx + ispconfig able to help me on this?

The current .htaccess I use with apache in order to remove index.php:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /ci/

RewriteCond %{REQUEST_URI} ^system.*
RewriteRule ^(.*)$ /index.php?/$1 [L]

RewriteCond %{REQUEST_URI} ^application.*
RewriteRule ^(.*)$ /index.php?/$1 [L]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L]

Update: I narrowed the issue down to this:
I can access my controllers/pages using index.php?/CONTROLLER but index.php/CONTROLLER does not work.

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