Curious that this issue should have cropped up with IE11, isn't it? There's a whole colourful discussion at http://answers.microsoft.com/en-us/ie/f ... 8970536cc1
and the general consensus of opinion is to add the offending website to your "compatibility list".
This, however, is an unacceptable solution. While, sure, on the one hand you get rid of the nagging "Scanstyles does nothing in Webkit/Firefox/Opera" prompt - and, in my experience, I have not been denied access to the page after acknowledging the prompt - if you add the website to the list of sites that IE11 will display in "compatibility mode", you will probably lose the "extra" CSS3 additions you might have implemented in your design.
So, the choice comes down to
(a) tolerate the nagging "Scanstyles does nothing in Webkit/Firefox/Opera" prompt - which is going to really going to turn away a section of your users who still think that IE11 is a good browser to work with; or
(b) get rid of the CSS3 additions because, if you've used them, they won't work in IE11 "compatibility mode"; or
For me, I'm not sure if this is a template issue or a Joomla issue (and, in my case, I'm using J! 3.2.0) but I would appreciate some guidance from the CMS team on this one. Thanks