Hi 祐哉,
私の母国語は日本語ではないので、この質問には英語で答えます。
This seems to be an issue with the "Open in figure window" functionality of the figure.
The workaround to open the figure in a figure window and center it is to do it programatically using the following MATLAB functions:
set(f,'visible','on'); % Display the figure in a figure window
movegui(f, 'center'); % Centers the figure window on the screen
The "movegui" function does not seem to be working when you open the figure in a window by clicking on "Open figure window" from the figure in the output pane.
Hope this helps.