Hello,
I've never experienced this problem before, and it just came to our attention because a client was trying to access our page and couldn't see much of the javascript. He was navigating to http://www.mysite.com, when we've always just gone to http://mysite.com.
There appear to be no problems server-side, as in both url's are pointing to the same place. There are also no errors on the page when it loads.
Has anyone had to deal with this before?
If your absolute urls reference http://mysite.com/js/file.js and there's no redirect in place then the JS files wouldn't get picked up properly, obviously.
Are you aware of Firebug and it's net tab? You can inspect and see if the js files are being retrieved.
It would help if you provided the real link.
Are you sending the JavaScript only to authenticated users?
If that's the case, then a user that authenticated on http://example.com, will not be able to access pages on http://www.example.com assuming you didn't make any other changes. This is because the cookies set on either (www. or roo) will not be sent to the server when the user navigates to the other.