It seems to be because the menu is a child of the header. The header has a z-index of 1000. The admin wrench also has a z-index of 1000. The admin wrench is in it’s own stacking context because of its fixed position. I’m not sure why the admin-wrench wins - I assume it’s because it comes last in the document.
The z-index of 1100 that is applied to the menu will only come into effect if the menu is overlapping other elements that are within its stacking context.