User show_windows and hide_windows to ensure all windows are shown and hidden properly.

src/calibre/gui2/main.py

@@ -398,9 +398,9 @@ class Main(MainWindow, Ui_MainWindow, DeviceGUI):
         self.card_a_view.connect_dirtied_signal(self.upload_booklists)
         self.card_b_view.connect_dirtied_signal(self.upload_booklists)
 
-        self.show()
+        self.show_windows()
         if self.system_tray_icon.isVisible() and opts.start_in_tray:
-            self.hide()
+            self.hide_windows()
         self.stack.setCurrentIndex(0)
         try:
             db = LibraryDatabase2(self.library_path)
@@ -515,7 +515,6 @@ class Main(MainWindow, Ui_MainWindow, DeviceGUI):
         pass
 
     def system_tray_icon_activated(self, r):
-        print r
         if r == QSystemTrayIcon.Trigger:
             if self.isVisible():
                 self.hide_windows()
@@ -644,7 +643,7 @@ class Main(MainWindow, Ui_MainWindow, DeviceGUI):
                     self.add_filesystem_book(path)
             self.setWindowState(self.windowState() & \
                     ~Qt.WindowMinimized|Qt.WindowActive)
-            self.show()
+            self.show_windows()
             self.raise_()
             self.activateWindow()
         elif msg.startswith('refreshdb:'):
@@ -1661,7 +1660,7 @@ class Main(MainWindow, Ui_MainWindow, DeviceGUI):
             self.spare_servers.pop().close()
         self.device_manager.keep_going = False
         self.cover_cache.stop()
-        self.hide()
+        self.hide_windows()
         self.cover_cache.terminate()
         self.emailer.stop()
         try:
@@ -1673,7 +1672,7 @@ class Main(MainWindow, Ui_MainWindow, DeviceGUI):
             time.sleep(2)
         except KeyboardInterrupt:
             pass
-        self.hide()
+        self.hide_windows()
         return True
 
     def run_wizard(self, *args):
@@ -1697,7 +1696,7 @@ class Main(MainWindow, Ui_MainWindow, DeviceGUI):
                         'choose <b>Quit</b> in the context menu of the '
                         'system tray.')).exec_()
                 dynamic['systray_msg'] = True
-            self.hide()
+            self.hide_windows()
             e.ignore()
         else:
             if self.confirm_quit():