I just see a very broken page in IE7 - 9 that doesn't get any better on refresh at all. The main problem is that you have some code above the doctype which will throw all versio0ns of IE into quirks mode and behave much like IE5.
Remove that code or place it where it should be as it looks like a broken fragment from somewhere.
I didn't see your link to the html5 shiv that ie8 and below need in order to recognise html5 elements unless you have it hidden away in one of your scripts.
Fix those issues first and then re-test. It may narrow the problem down.
I believe moderniser contains the shiv for IE anyway so you don't need the extra shiv. However you should ensure that the js is above the css in the html otherwwise there won't be anything created for IE to style and is probably why you get the FOUC.