I just migrated from the Atlas July CTP to ASP.NET 2.0 AJAX Extensions 1.0.  After following all of the instructions on the AJAX site, my web site still showed tons of errors.  I'm using a Web Site, not Web Application, with a ScriptManager in a WebForm that uses a MasterPage.   Every page shows errors on AJAX tags. 

Yes, I removed the Atlas DLL.  No, my web.config is not messed up.  Something else is wrong here.   I found a "fix".   The sequence of steps seems a little odd to me, but I did't care, it worked.  However, the problem resurfaced when I closed my MasterPage.

More searching led me to a great alternative to a true solution.   An ASP.NET Forums post had some back-and-forth on the topic.  Ultimately, the best solution at this point is to change the tagprefix to "ajax".   This works great, and, in fact, I like it better because it separates the ajax controls from the standard asp controls.

<add tagPrefix="ajax" namespace="System.Web.UI" assembly="System.Web.Extensions, Version=1.0.61025.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35"/>