I tinkered with the css a little and found the following updates made it render correctly in IE6.
In the CSSMenuWriter > cssmw > menu_ie.css file find the style titled ul#cssmw li.hover a {. In here add in the following three values into this style so it looks like this:
ul#cssmw li.hover a {
background-color: #187fc4; /* blue */
color: #f0b010; /* gold */
font-weight: bold;
text-decoration: none;
/* three additional values are below this comment */
display:inline-block;
border-bottom: solid 1px #103689; /* dark blue */
margin-bottom: -4px;
}