If you add any custom HTML to render at the end of HEAD, the real estate that it takes is then removed from the bottom of the XHTML editor pane, hiding the bottom of the scroll bar and the last few lines of the page body (see screenshots).

By drag-selecting to the end of the content in the editor, the view of the page shifts, revealing the missing content and scrollbar, but hiding the banner. Based on how it looks, Confluence is placing >100% viewable area within the window, causing the footer to overlap the bottom of the editor.