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The issue is that the front-most window in full screen mode is not actually the main document window. Notice how when you move the mouse pointer to the top of the screen to reveal the menu bar, the toolbar slides down in front of the main window.

In most cases, you can change references to the:
front window
to instead say:
first document window of default document
That works in normal and full screen modes. The only problem is when you have another document (say your Archive) open and in full screen. My alternative phrasing won't reference that other document.