I was several versions behind, so I decided to upgrade my site to the latest DNN version by setting up a new site under a temporary subdomain.  I had everything working great, so I added my main domain as a portal alias, then set it to the primary alias, then switched over the DNS.  Now when I hit the site via the "new" main domain URL, the site loads but certain features do not work properly.  E.g. instead of getting a login modal I get sent to a login page, the Edit Page button will not go into edit mode, when I go to site settings the tabs are all dumped out to one page and the sections within do not expand/collapse.  If I return to the first URL (the original one where the site was installed under) all works normally, but not via the new/main domain.

Any ideas as to what causes this, and how I can resolve it?

 

Yes to all 3. I even tried different browsers, same result.

Here are the URLs in case it helps (apologies if inappropriate):
Temporary (working) alias: http://newsite.fantasydraftassistant....
Permanent (problem) alias: http://fantasydraftassistant.com/dnn

Most obvious difference without a login is the login button, which launches modal on the old but redirects to a page on the new (I'm guessing some kind of fallback).

Indeed, it looks like today neither alias works correctly, and they both redirect to a page instead of the modal.  I can no longer go into edit mode using either URL, so the problem is worse now.  I tried several things last night but apparently they made it worse rather than improving things.