I have several pages in my site with ModalPopupExtenders in them. Generally, the MPE markup is at the end of the aspx. We've started to see that these popups produce inconsistent behaviour in IE9 (sometimes popping up as expected, sometimes not). I tracked it down to the fact that the client side sys.Application framework is firing the initialization and load events before all the script tags in the body of the document have been processed, so our popups aren't initialized yet when the page_load function tries to pop them up.
This is the init code that lives in a script tag at the end of the dom, and doesn't get run until after the page_load event, because the page is not yet "complete":
Sys.Application.add_init(function() { $create(AjaxControlToolkit.ModalPopupBehavior ...This doesn't look like it's specific to MPE's, but could affect any control that is expecting to have an instance created during init. Is this new to IE9?