Server URL problems
In addition to the troubleshoot section within the user guide (http://www.codeigniter.com/user_guide/installation/troubleshooting.html try setting the type ) which suggests appending an '?' to your URLs as a last result try forcing type:
<FilesMatch "^index.php$"> SetHandler application/x-httpd-php AcceptPathInfo On
Sometimes Apache just needs to be told that 'my.php' is actually a PHP file in order for path info to work correctly I believe it has something to do with security in Apache 2 ;)
For more info have a read of this thread over at DevShed http://forums.devshed.com/apache-development-15/acceptpathinfo-apache2t-34197.html?&highlight=PATH_INFO