Do you have any div with relative or absolute positioning without the z-index property?!
I had this issue once, and it when the menu get behind somehing is most of the times because the z-index.
If you have a div or something near the menu and it doesn't have z-index it can hide the menu in IE's.
I really don't know if this helps anything and if it was this kind of answer you were looking about.
Best regards, and good luck in your work