Precondition:
I have an aspx-page with iframe inside. This iframe points to the url handled by MVC on the same site (it\'s hybrid site, both standard ASP.NET and ASP
I have encountered this same situation in the wild. Basic symptoms:
I found that it can often be prevented by delaying the execution of the script code until onload or DOMContentLoaded... Not much help I know but this is one of the most difficult IE scripting bugs I have ever encountered. I upped the score of your question, hope it will be found by others as well and we can get a more detailed answer.
Also see this question: Error in Internet Explorer 9 (not earlier versions or other browsers) when including jQuery in an iframe