Hi Adam -
When I look at your page with the IE Developer Toolbar - it is showing the li has a background color of #fff. This might be how IE initializes it if it is not set.
Have you tried setting the li in the css? Something like:
ul.MenuBarHorizontal li {background-color: transparent;}
or initialize it at the top of your css:
li {background-color: transparent;}
If this turns out to be the issue, you might want to add your support to get QT to initialize their CSS in v5
here.