[eluser]Rick Jolly[/eluser]
Could be that you're redirecting to the root directory in your htaccess. See below:
Code:
RewriteEngine On
# do you have RewriteBase set to a subdir or is the subdir prefixing the index.php/$1?
RewriteBase /your_subdirectory
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php/$1 [L]
What is your base_url set to?