This not only happens when launching gedit in "different ways" (i.e. one clicking on a file and the other from a terminal).
This also systematically happens when opening multiple files all by double clicking in Nautilus if the current gedit window exceeds even the slightest bit outside of the current screen.
However I've just observed it happen even though the current gedit window was fully within the screen.
Please see also #777292
This not only happens when launching gedit in "different ways" (i.e. one clicking on a file and the other from a terminal).
This also systematically happens when opening multiple files all by double clicking in Nautilus if the current gedit window exceeds even the slightest bit outside of the current screen.
However I've just observed it happen even though the current gedit window was fully within the screen.