After I have checked this bug (https://sourceforge.net/tracker/?func=detail&aid=3300797&group_id=156956&atid=801864) and can confirm it is fixed I have noticed that this is a more generic problem. Other subwindows like the attribute menu or creating a new object aren't on the first layer too. But hiding the copy subwindow could be a problem too.
But there is a solution that solves all of these problems: What I would change:
1. The last opened subwindow orders itself to the top.
2. It should be possible to reorder these subwindows. This should be happen for example if I click the menus on my panel. The last clicked subwindow will reorder itself to the top.