Я думаю, что вы пропустили '?'. RewriteRule ^(.*)$ /index.php?/$1 [L]
Это рекомендуемый CI шаблон .htaccess (или, по крайней мере, год назад), и именно ?
является основным отличием между ними.
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
#Removes access to the system folder by users.
#Additionally this will allow you to create a System.php controller,
#previously this would not have been possible.
#'system' can be replaced if you have renamed your system folder.
RewriteCond %{REQUEST_URI} ^system.*
RewriteRule ^(.*)$ /index.php?/$1 [L]
#Checks to see if the user is attempting to access a valid file,
#such as an image or css document, if this isn't true it sends the
#request to index.php
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L]
</IfModule>