How to reproduce the problem:
Web Server installed under .NET 4.0 version possible caused IE11 can not recognize User-Agent request header from your web server.
Solution:
Modify or Add file in your web site. ~\App_Browsers\w3cvalidator.browser.
(File link backup : https://www.dropbox.com/s/85887zvntlxe3fl/w3cvalidator.browser?dl=0)
Read this to get more detail. http://blogs.telerik.com/aspnet-ajax/posts/13-12-19/how-to-get-your-asp.net-application-working-in-ie11