Codeigniter 404 Error - Controllers Not Found

[eluser]Unknown[/eluser]
I'm trying to get a development server working and have a fresh install of Ubuntu 13.10 with apache2 and php5 installed on it. On a fresh codeigniter install, the latest available (2.2.0), I can navigate to the default controller index function by using the base url, as configured in the config.php.

i.e. http://example.com/ci/ -> brings you to the default controller, welcome.php and the index function.

However, when navigating to http://example.com/ci/welcome/index or http://example.com/ci/index/ I get a 404 error. It seems to be that apache is seeing these as directories instead of reading the codeigniter controllers.

Everything in Apache is set to the default settings as well as php.ini, I have no .htaccess enabled because the ones I have tried have been unsuccessful.

These are the modules enabled given by phpinfo():

Code:

core
mod_so
mod_watchdog
http_core
mod_log_config
mod_logio
mod_version
mod_unixd
mod_access_compat
mod_alias
mod_auth_basic
mod_authn_core
mod_authn_file
mod_authz_core
mod_authz_host
mod_authz_user
mod_autoindex
mod_deflate
mod_dir
mod_env
mod_filter
mod_mime
prefork
mod_negotiation
mod_php5
mod_setenvif
mod_status

Any ideas?