[eluser]solvo[/eluser]
Hey dnc,
I've successfully tested the latest version CodeByrner using modrewrite to remove the index.php from URLs. Should be all set for either way you choose to use it.
I've also included a .htaccess file with the basic rules to allow you to go ahead and use modrewrite. The rules are commented out so that they don't do anything "out-of-the-box", just like CodeIgniter doesn't come using modrewrite, but the file is included as a convenience as I expect just about everyone removes the index.php from their URLs. So that should make life at least a tiny bit easier.
Let me know if you get a chance to play with it and have any thoughts.