A notification window appears not only in the right bottom corner of the UGENE main window. It could appear to the left-top or to the right-bottom of the corner. If you change the main window size by dragging the left top corner, the notification window will change its place of occurrence relative to the main window. If you change the main window size by the expand button, the notification window also will change its place unexpectedly (off-screen maybe).
Dragging the main window by its title sets the notification window to its normal place.