Internet explorer doesn't display sites correctly unless they are trusted

This is an odd problem. On the reference image prior to it being sysprep'd and captured, going to certain sites (e.g. lifehacker.com) the menus, all pictures and advertisements display just fine. But once capture and deploy that image those sites stop working
the way they should. I made sure the unattend file was making zero changes to IE and I even disabled the IE configuration app that I made with IEAK to ensure that IE was being setup as is out of the box, but something is changing the way it operates and it
fails to work the way it did before it get deployed to a client. I don't have any extra add-ons and no tracking protection lists.
The big problem is it causes compatibility issues with lots of sites, such as menus not appearing when you hover like they should. I even tried building a clean machine from the Microsoft media directly and creating IEAK packages from that, a totally clean
machine. That didn't work either.
Anyone else have weird problems like this before?
If this post is helpful please vote it as Helpful or click Mark for answer.

Windows 8.1 IE 11. Yesterday I built a new image with all the latest updates released yesterday.
My "Base Package" of apps is:
Visual Studio Tools 2010
Chrome
Firefox
Adobe Reader
Flash Player
Java RE
7-ZIP
BOX
VLC Player
The reference image itself contains Office 2013. This issue only affects Internet Explorer in normal view, if you use Private Mode the same site that didn't work, works just fine. I've tried experimenting with not enabling any add-ons and using "Reset"
in IE, but nothing works.
I am using copy profile, but I can assure you the administrator profile works just fine with all sites in the reference image before it's sysprepped and captured. But then again IE works fine until after the first reboot when deployed to a client.
If this post is helpful please vote it as Helpful or click Mark for answer.

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