[eluser]BrianDHall[/eluser]
It sounds like it must be something related to your .htaccess file - here's mine, you might try it:
Code:
RewriteEngine on
RewriteCond $1 !^(index\.php|images|css|js|robots\.txt|favicon\.ico)
RewriteRule ^(.*)$ /index.php/$1 [L]
Obviously you'll need to add the directories/files that aren't CI. See if this makes any difference at all.
I'm afraid I don't even fully understand modrewrite, I just kept trying different code snippits until I got one that worked for me