Looking at the doc you posted it seems that your IE specific css might not be linked properly. You currently have it like this:
@import url("CSSMenuWriter/cssmw/menu_ie.css");
The other css files on this page are linked to like this:
@import url("../CSSMenuWriter/cssmw/menu.css");
You should be able to get it working by adding the ../ to the beginning of the menu_ie.css file like this:
@import url("../CSSMenuWriter/cssmw/menu_ie.css");