Ajax Control Toolkit has just stopped working recently. I didn’t understand why because every other site including the example site just worked well. So I checked the web.config and everything was correct. I’ve created a test page inside the web project, and that did not work. I realized that every single page that contained ajax did not work.
Well, I finally compared the web.config file to the latest SVN version. The main difference were the rewrite rules for IIS7, so I started checking them. Now I know that the reason of misbehavior was a rewrite rule that was applied to all the pages and redirected the ajax calls to a wrong place.
My advice: always check your rewrite rules. Just disable them all and enable them one by one.