Same problem. Just rolling over a tiny portion of the mostly hidden window pops the whole thing to the foreground. Makes it completely useless to have anything but active or minimized. Used to be that clicking anywhere brought it forward, also not desirable, but tolerable.
I blame gnome/gtk for forcing every app to be their own window manager. Now every desktop app looks different and behaves in random ways instead of how I set my window manager. Chrome has started doing this too for some of it's sub-windows. Pretty soon it will be the whole browser.