Changed the type of the hidden panel to GTK_WINDOW_TOPLEVEL, so that it is not visible in fullscreen applications.
--- a/panel/panel-window.c
+++ b/panel/panel-window.c
@@ -2163,13 +2163,14 @@
       /* create the window */
       panel_return_if_fail (window->autohide_window == NULL);
       popup = g_object_new (PANEL_TYPE_BASE_WINDOW,
-                            "type", GTK_WINDOW_POPUP,
+                            "type", GTK_WINDOW_TOPLEVEL,
                             "decorated", FALSE,
                             "resizable", TRUE,
                             "type-hint", GDK_WINDOW_TYPE_HINT_DOCK,
                             "gravity", GDK_GRAVITY_STATIC,
                             "name", "XfcePanelWindowHidden",
                             NULL);
+      gtk_window_set_keep_above (popup, TRUE);
 
       /* move the window offscreen */
       panel_base_window_move_resize (PANEL_BASE_WINDOW (popup),