If the popover is given an initial position which is left unchanged, some content in the same area gets mapped afterwards (and its windows raised), and the popover is later shown, the GdkWindows that were shown/raised in such content would be left above the popover one.

This is visible in gnome-maps master, where the popover points to an entry inside a revealer. The popover first get a correct initial position (eg. where the revealed entry would lie), but the entry and other revealer contents would be actually mapped when the revealer is shown, making all windows there raised above the popover.

_gtk_window_set_popover_position() is called in various places where the position or visibility of a popover might have changed, but is usually a no-op if the position didn't change at all. I'm attaching a patch to have it only avoid gtk_widget_queue_resize() in those situations, still realizing/showing/raising the GdkWindow if necessary.