After an exhaustive search, I found out how to successfully prevent an intranet site from rendering in compatibility mode in IE9 on this blog:
From Tesmond's blog
There are 2 quirks in IE9 that can cause compatibility mode to remain in effect.
The X-UA-Compatible meta element must be the first meta element in the head section.
You cannot have condtional IE statements before the X-UA-Compatible meta element.
This means that if you use Paul Irish's wonderful HTML5 Boilerplate then on an Intranet with default IE9 settings your website will display in compatibility mode. You need to change the start of the boilerplate from the following:-
<!doctype html>
<!--[if lt IE 7]> <html class="no-js ie6 oldie" lang="en"> <![endif]-->
<!--[if IE 7]> <html class="no-js ie7 oldie" lang="en"> <![endif]-->
<!--[if IE 8]> <html class="no-js ie8 oldie" lang="en"> <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en"> <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
to:
<!doctype html>
<html class="no-js" lang="en">
<head>
<meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
<meta charset="utf-8">
与恶龙缠斗过久,自身亦成为恶龙；凝视深渊过久,深渊将回以凝视…
