CodeIgniter sub-sub-folder controller works localhost but not on server

I'm having troubles with this structure only on server environment:

controllers    
    -> Controller_home.php    
    -> folder 1/
      -> Controller_1.php
      -> Controller_2.php
      -> folder 2/
        -> Controller_3.php

Controller.home.php works fine

Controller_1.php works fine

Controller_2.php works fine

Controller_3.php doesn't work - it appears my custom 404 page error

I'm using CodeIgniter 3.0 version, and previously I had trouble with the required first letter of each controllers to be uppercase. So I rename all my controllers and models files to use the first letter as uppercase.

I thought the problem I'm having now could be due to the folders inside controllers/ not be uppercase, but it ain't because of that.

I repeat that the structure works on local environment.

Edit: As requested, my .htaccess file:

Options -Indexes
Options +FollowSymLinks

# Set the default file for indexes
DirectoryIndex index.php

<IfModule mod_rewrite.c>

    # activate URL rewriting
    RewriteEngine on

    # do not rewrite links to the documentation, assets and public files
    RewriteCond $1 !^(index\.php|public|robots\.txt)

    # do not rewrite for php files in the document root, robots.txt or the maintenance page
    RewriteCond $1 !^([^\..]+\.php|robots\.txt)

    # but rewrite everything else
    RewriteRule ^(.*)$ index.php?/$1 [L]

</IfModule>

<IfModule !mod_rewrite.c>

    # If we don't have mod_rewrite installed, all 404's
    # can be sent to index.php, and everything works as normal.

    ErrorDocument 404 index.php

</IfModule>

<IfModule mod_expires.c>

    ExpiresActive on

    ExpiresByType image/jpg "access plus 1 month"
    ExpiresByType image/jpeg "access plus 1 month"
    ExpiresByType image/gif "access plus 1 month"
    ExpiresByType image/png "access plus 1 month"
    ExpiresByType image/bmp "access plus 1 month"

</IfModule>

My Controller_3.php (it's actually a Customers controller) code:

<?php if (!defined('BASEPATH')) exit('No direct script access allowed');

class Customers extends CI_Controller
{
    public function __construct()
    {
        parent::__construct();


    }

    public function index()
    {   
        $this->load->view('backend/customers/index');
    }
}
?>

Edit 2: My complete (so far) route file:

$route['translate_uri_dashes']                  = TRUE;
$route['default_controller']                    = 'home/login';
$route['404_override']                          = 'home/error';

$route['app/entities/index']                    = 'backend/entities/index';
$route['app/suppliers/index']                   = 'backend/suppliers/index';
$route['app/administration/customers/index']    = 'backend/administration/customers/index';