Replicates Content Within Tags on IE9 Compatibility View

[chryton]

After some extensive debugging of open/closed tags on our templates, I am noticing if my current project is being viewed in IE9 Compatibility, HTML5Shiv will replicate code within the last child of elements, specifically list-items within a header element. This problem has brought to my attention by a client who can only use IE 9 via an intranet. I have already set the headers via the htaccess file to X-UA-Compatible "IE=Edge,chrome=1" env=ie.

You can take a look at this link where it is doing this throughout the header in IE 9 Compatibility Mode: http://meade.madmonkdev2.com/
But, oddly enough, it is not doing the same on interior pages:
http://meade.madmonkdev2.com/about/

We have tried commenting out all the elements on the page except for the header and what happens is it will duplicate the commented-out HTML regardless. If you comment out the header element or both section elements within the header then display the page, the content is not replicated within the DOM.

I am wondering if there is either a structural issue or if there is an actual issue with HTML5Shiv as this happens with just the shiv (not just Modernizr which I had used initially).