Clean URLs and Javascript problem

I am running a site on a Rackspace server. The domain is hosted else where and a subdomain is pointing to the IP on the Rackspace server.

Previously, I had clean urls disabled on Drupal. However, clean urls is necessary to have imagecache work. I enabled clean urls and the site functions normally, except...all javascript seems to be not work. Tables (such as taxonomy) are not drag able, javascript uploads default to older methods and views interface runs without javascript. Any thoughts on what would cause this problem?