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Changing the key org.gnome.desktop.input-sources.per-window to "On" will automatically close the pop-up window by clicking on it. When the key is changed to “Off”, the behavior is normal. My environment from configuration: org.eclipse.swt.internal.deviceZoom = 100 org.eclipse.swt.internal.gdk.backend = x11 org.eclipse.swt.internal.gtk.theme = Ambiance org.eclipse.swt.internal.gtk.version = 3.22.30 org.eclipse.swt.internal.webkitgtk.version = 2.28.0 os.arch = amd64 os.name = Linux os.version = 5.3.18-050318-lowlatency Ubutntu OS 18.04 with the latest updates.