I often have to open the menu from the system tray because it is obscured by any existing topmost window. Should the menu not open on top, as happens with system tray menus and taskbar jump lists, etc?
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By default, it shouldn't be behind anything. If you have a window set to 'always on top' it'll display over the PA.c Menu. What is it behind?
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VLC media player or a PiP video, for example, which are "always on top" by default.