Drupal pages all redirecting to main web page

Hey everyone,
I have a customer who has a Drupal site (6.19 I think?) hosted at GoDaddy.com, and we have a website that uses Drupal for portions of the site. The site is laid out like this:
examplewebsiteurl.com/ <-- The non Drupal portion of the site
examplewebsiteurl.com/cms <-- This being where Drupal is installed
The problem is that links to any of the /cms pages take about 10 seconds and then bring up examplewebsiteurl.com/ instead with no visible error messages. Attempting to visit examplewebsiteurl.com/cms/index.php results in a too many redirects error in my web browser.
GoDaddy support insists the problem is not on their end and that the drupal installation is fine, and that they think the problem is with the sites "permalink".
Does anyone have any ideas what might be going on and how I can go about fixing it?
Thanks.