In the code, I see where you have two separate menus, now:
<?php require_once("CSSMenuWriter/cssmw0/menu.php"); ?>
<?php require_once("CSSMenuWriter/cssmw/menu.php"); ?>
Have you tried removing, say, the bottom menu just to see if the top one would work? I would start by taking one out to see if it is, in fact, the other one causing the problem. Once we determine that, it will be easier to hunt down what is going on.
My suspicion is that that each CSS menu writer instance has a Z-index set high enough that may cause an issue with the other.
Let me know what happens when you take a menu out and then try it.