title: Only default controller is working, other controllers/routes are not
body: <p>Just recently upgraded from Code Igniter 2.2 to Code Igniter 3.</p>
  
  <p>Website is plaster.tv. The homepage works however any other URL is routed to this default_controller even though other routes are specified:</p>
  
  <p><strong>/application/config/routes.php</strong></p>
  
  <pre><code>$route['default_controller'] = "home";
  $route['404_override'] = '';
  $route['translate_uri_dashes'] = FALSE;
  
  $route['login'] = 'login';
  $route['signup'] = 'signup';
  $route['main'] = 'main';
  $route['sendResetEmail'] = 'sendResetEmail';
  $route['resetPassword'] = 'resetPassword';
  </code></pre>
  
  <p>Internal pages which is handled by other controllers, e.g. plaster.tv/signup doesn't work, but plaster.tv/?c=signup works. </p>
  
  <p><strong>/application/config/config.php</strong>:</p>
  
  <pre><code>$config['base_url'] = 'http://www.plaster.tv/';
  $config['index_page'] = '';
  $config['uri_protocol'] = 'REQUEST_URI'; //worked using AUTO in CI 2.2
  $config['url_suffix'] = '';
  $config['subclass_prefix'] = 'MY_';
  $config['composer_autoload'] = FALSE;
  $config['permitted_uri_chars'] = 'a-z 0-9~%.:_\-';
  $config['allow_get_array'] = TRUE;
  $config['enable_query_strings'] = TRUE;
  $config['controller_trigger'] = 'c';
  $config['function_trigger'] = 'm';
  $config['directory_trigger'] = 'd';
  </code></pre>
  
  <p><strong>/application/controllers/Home.php</strong>:</p>
  
  <pre><code>&lt;?php if (!defined('BASEPATH')) {
      exit('No direct script access allowed');
  }
  
  class Home extends CI_Controller
  {
      public function __construct()
      {
          parent::__construct();
          $this-&gt;load-&gt;library('form_validation');
      }
  
      public function index()
      {
      //... this part works
      }
  }
  </code></pre>
  
  <p><strong>/application/controllers/Signup.php</strong>:</p>
  
  <pre><code>&lt;?php if (!defined('BASEPATH')) {
      exit('No direct script access allowed');
  }
  
  class Signup extends CI_Controller
  {
      public function __construct()
      {
          parent::__construct();
      }
  
      public function index()
    {
  //... this class is never called when the URL is http://www.plaster.tv/signup but is called when the URL is http://www.plaster.tv/?c=signup 
   }
  }
  </code></pre>
  
  <p>Hope someone could help me figure this out.</p>