For starters, try to rename Help to something else...
Renaming "Help" to something else helps ... "Search" bar disappears and my own menu starts to work, although I'd prefer to have menu item named "Help"...
Another strange thing is that my first menu item "File" gets replaced with the application menu (submenu is mine).
Nothing like that happens to the TheIDE. And you do not seems to have any MacOS-specific code ...
This is a little bit weird ...