I am having this issue as well.
In my old code I had this._Menu.DomElement.style.zIndex = 999999; and it worked fine. After the upgrade, I changed it to this._Menu.get_element().style.zIndex = 999999; and it does not seem to do anything. I checked the html of the dom element and it looks like everything under it is just a li or ul
Do I have to set the zIndex somewhere else?
The issue appears to be happening on the public demo as well:
If you put your mouseover the file option of the horzintal menu, the menu will go under
It does not seem to happen in the old demo: