...well it does not ignore them, it puts them into relation to the window on which the last activity (focussed element) was executed. In other word: the next popup is positioned relative to the coordinates of the Yes/No Popup.
We do not want to "just change" this logic because it makes sense in a lot of cases (the next popup is positioned "in the neighbourhood" of the previos popups) and there are users expecting this behaviour.
What you can do: adjust the coordinates accordingly: e.g. assigne left/top as "-200,-200" so the the follow on popup is positioned in a smarter way. Maybe this is a bit a workaround, but it works! ;-)