Same problem for me. If you change something in theme magic and create a new theme (that goes under local folder) the menu disappears... please help (working on localhost).
example:
1- change the theme and save as a new one called NEWTHEME
2 - in the template settings, in "theme" tab, set NEWTHEME as theme
3 - save
4 - HEADER IS GONE "Block [header/header_NEWTHEME] not found!
5 - creating a copy of the default layout and saving it as NEWDEFAULTLAYOUT
6 - selecting it into the "layout" tab (with newtheme in the theme tab)
7 - HEADER IS GONE "Block [header/header_NEWTHEME] not found!
Copying the template.less file into local folder (local/less/NEWTHEME) doesn't change anything...