With fix for RT-28775, the Popup x, y coordinates no longer specify the upper left corner of the window, but some inner point of it. This means that any conversion from window coordinates to screen coordinates and back which uses only the Window x, y position won't work for these shifted popup windows. All such conversions in Scenegraph code were fixed in RT-29728 including the Node.localToScreen and Node.screenToLocal conversion methods. Similarly usage of Window.getX() and Window.getY() usage should be investigated and fixed in controls code. Whenever possible the Node.localToScreen and Node.screenToLocal should be used.