The initialization of ediff control window is affected by the fullscreen in window-system-default-frame-alist.
(cl-pushnew '(w32 (font . "Consolas-14")
(fullscreen . maximized))
window-system-default-frame-alist)
So that for each new frame, it will try to make the frame fullscreen including the edif control window. And when the ediff control pop-up on the right-side
of the screening from top to bottom (like fullscreen). When I type "?", it shows the help
message windon. I type "?" again, it gets back to the control windown,
and now the window is on the top-right of the screen as a small window.
I was suggested by Stefan Monnier:
(with-eval-after-load 'ediff-wind
(push '(fullscreen . nil) ediff-control-frame-parameters))It solves the problem.
I think the default behavior of the initialized ediff control window should not be full-screened. I suggest to add '(fullscreen . nil) to ediff-control-frame-parameters as default.