If you have not solved your problem yet , the link below might be useful

I ran into the same problem, with catastrophic consequences because of my heavy ajax usage.. My website loaded, but no clicks would work, update panel timers would not execute et etc..

Check this article for reference.

http://www.codeguru.com/csharp/.net/net_asp/tutorials/article.php/c12927/

He essentially asks us to load the script manager dynamically( if not available in the page.controls collection) during the "preinit" of the Page...