I don't know if is related, but I apreciate similar problem. Running debian wheezy amd64 as VirtualBox guest on Windows 7 64 as host, with 3d aceleration enabled.
When I view this site http://www.html5rocks.com/en/tutorials/webcomponents/shadowdom/ the view zone flicker showing background desktop and minimize window not hide the page view. In this site http://ricostacruz.com/jquery.transit/ after scroll and intereract with the page corrupt the view. When navigate to another site using this tab all gnome shell corrupt and reboot the system and init a new gnome session show a gnome session corrupted. If I halt the virtual machine and turn on the problem dissapear until the steps described. If I disable 3d aceleration in virtual machine, gnome run in fallback mode and the problem not occur. The problem is the same using Google Chrome installed from google site.
