For what it's worth, I have the same issue with a vertical menu on a master page that worked fine in Beta 1 - dynamic submenu is clearly being generated as it blanks out part of the main content area, but is invisible. I have the menu in a div with an ID of 'navbar' which in the CSS stylesheet has the following:
#navbar
{
position: absolute;
top: 20%;
width: 15%;
}
The main content area div is similarly positioned with a left of 15%. I seem to recall having to add a z-index of -1 on the main content area for this to work in Beta 1, but this has no effect in Beta 2.
Removing the id from the navbar div does indeed cause the dynamic submenu to work as intended, but obviously screws up my layout. I really don't want to have to use tables.
Jon