Not a real answer but could help somebody else find a work around for this bug in IE.
Page containing iframes
<link href="style.css" rel="stylesheet">
Iframe pages
<link href="style.css?frameX" rel="stylesheet">
The param frameX prevents IE from caching the css page and thus the iframe has responsive layout independently from the other pages. This is just a hack(horrible one) and to help somebody else find the answer to this problem.
Sample files
Index.html
<!DOCTYPE html>
<html lang="en">
<head>
<title>Title</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="style.css" rel="stylesheet">
</head>
<body>
<p></p>
<hr>
250px frame
<iframe frameBorder="0" src="frame1.html" height="100" width="250" id='frame_1'></iframe>
<hr>
350px frame
<iframe frameBorder="0" src="frame2.html" height="100" width="350" id='frame_2'></iframe>
<hr>
390px frame
<iframe frameBorder="0" src="frame3.html" height="100" width="390" id='frame_3'></iframe>
</div>
</body>
frame1.html
<!DOCTYPE html>
<html lang="en">
<head>
<title>Title</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="style.css?page=frame1" rel="stylesheet">
</head>
<body>
<p></p>
</body>
</html>
frame2.html
<!DOCTYPE html>
<html lang="en">
<head>
<title>Title</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="style.css?page=frame2" rel="stylesheet">
</head>
<body>
<p></p>
</body>
</html>
frame3.html
<!DOCTYPE html>
<html lang="en">
<head>
<title>Title</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link href="style.css?page=frame3" rel="stylesheet">
</head>
<body>
<p></p>
</body>
</html>
style.css
iframe{display:block;}
@media (max-width: 8000px)
{
body p:before {content: "bigger than 550px";}
}
@media (max-width: 550px)
{
body p:before {content: "max550";}
}
@media (max-width: 450px)
{
body p:before {content: "max450";}
}
@media (max-width: 350px)
{
body p:before {content: "max350";}
}
@media (max-width: 250px)
{
body p:before {content: "max250";}
}
<style>
tags of the html file to be displayed in the iframe, as opposed to an external sheet linked to on the page with the iframe, and IE9 is rendering all of the CSS, even when inside a query that should be ignored, on load, then rerendering correctly if I scale my browser some. – Bael