This may help, as I was having the same issues as you guys. In the Solution Explorer, check your Start Options. Browse to References, then highlight the AjaxControlToolkit and press the Update button. Make sure you have your pages closed with the controls that are showing errors. Next, rebuild your website. Finally, open your page and see if this worked. I tried a few things and this was the step that seemed to make all of my controls come back to life. I'm running VS2008 sp1 ASP.NET 3.5 Ajax Control Toolkit SP1.
Let me know if I answered this for you guys, and good luck!
Todd