I was having the same problem… a little trial & error and I found that on the Stylesheet – style.css, the version 2.0.0.4 code was missing position:relative; that was contained in the version 1.9.9.7 code.
Original 2.0.0.4 Code
ul#front_menu{float:left;text-transform:uppercase;margin-top:-4px;height:36px !important;z-index:-10;}
My Modified 2.0.0.4 Code
ul#front_menu{float:left;text-transform:uppercase;position:relative;margin-top:-4px;height:36px !important;z-index:-10;}
Adding that to style.css seems to have fixed the problem for me. Hopefully it will help you out as well.
As a reminder, you’ll need to refresh your page after doing so to confirm if the changes actually took place.
