results from site_url()

Did you remove 'index.php' from index_page config setting in /application/config/config.php? That also needs to be done.
$config['index_page'] = '';

Code:

/*
|--------------------------------------------------------------------------
| Index File
|--------------------------------------------------------------------------
|
| Typically this will be your index.php file, unless you've renamed it to
| something else. If you are using mod_rewrite to remove the page set this
| variable so that it is blank.
|
*/
$config['index_page'] = 'index.php';