Does the directory need to be int he root folder, can it not be further down the hierarchy? By having a directory with the same name as your controller in the root directory, your web server is serving up the directory instead of normal CodeIgniter routing.
If it's an absolute must to have the folder in the root, then you would need to change your .htaccess file to ignore requests which match the directory name for that directory (and any others which match controller names).
There's an answer for this already, as well as a good example on the Drupal website which I've put in below in case it gets moved
=========[ start of .htaccess snippet]==========
<IfModule mod_rewrite.c>
RewriteEngine on
#
RewriteCond %{REQUEST_URI} !^/yourDirectoryName
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php [L,QSA]
</IfModule>
====================[ end ]=====================