I'm not sure. The javascript code usually corrects offset problems like this in IE6, so it isn't working properly for some reason.
I noticed a stray: <![endif]> tag before </head>... that might cause some issues not sure what....
If you apply the menu to a new page without making hand edits does it work? Once you edit by hand it is like finding a needle in a haystack to see what might cause the issue especially in a browser as finicky as IE6.