[eluser]Aken[/eluser]
I don't think needing to use chdir() is very common with CodeIgniter applications. So while it isn't "expected" in that sense, it is not an error.
The Loader class does use relative paths, which start with the APPPATH constant defined in the index.php (using the $application_folder variable).
You can solve this by setting your application (and maybe your system) path to the full absolute location in index.php.
Code:
$application_folder = '/Users/aken/Localhost/example.com/application';