This event is called the "Hanging Menu" effect. The "Hanging Menu" effect is an IE-only bug that can be solved by placing the Linking Code instance of the menu right before the </body> TAG.
In more detail, IE is loading pages in a different way that other browsers. It first loads the structure and then it loads all the text and images. The result of this is that you get the "awmAnchor" with the structure (hence the menu shows), but the whole table is still empty and concentrated in the top-left conrner (and your Anchor is there too!).
You may have noticed cases where you have pictures in your webpages and the image-holder box changes size when it loads the image (it's the same thing).