We've seen a few issues recently where customers were experiencing very slow async postbacks via an UpdatePanel, but only in Internet Explorer. Other browsers worked fine. (When I say "very slow", I mean in the neighborhood of 30 seconds!) The cause for this isn't a mystery to us.
Because of the way our HTML viewer (mshtml.dll) was designed, Internet Explorer is slow to iterate through large DOM collections. As it happens, the PageRequestManager class has a method called _destroyTree that does just that. It uses a for loop to iterate through all of the DOM nodes in the UpdatePanel's DIV. It does this on the client (the browser) before the request to the Web server is ever kicked off, and if you have a large DOM in your UpdatePanel, you might see a very long delay in Internet Explorer when this occurs.
If you're experiencing this kind of problem, I have good news. We've fixed this for the next version of ASP.NET, and we also have some code that you can use in your applications now to mediate the problem. You can find the updated code in our Knowledge Base at http://support.microsoft.com/?kbid=2000262.
Update 9/29/2009:Removed the code from this blog post and referenced KB instead. We did this so that we can service the KB article without having to update this post in the future.