Proper quit sequence:

close MainWindow and quit the app instead of sys.exit()

src/bitmessageqt/__init__.py

@@ -2280,6 +2280,7 @@ class MainWindow(Window):
             QtCore.QEventLoop.AllEvents, 1000
         )
         shutdown.doCleanShutdown()
+
         self.updateStatusBar(_translate(
             "MainWindow", "Stopping notifications... %1%").arg(90))
         self.tray.hide()
@@ -2288,20 +2289,21 @@ class MainWindow(Window):
             "MainWindow", "Shutdown imminent... %1%").arg(100))
 
         logger.info("Shutdown complete")
-        super(MainWindow, self).close()
-        # return
-        sys.exit()
+        self.close()
+        # FIXME: rewrite loops with timer instead
+        if self.wait:
+            self.destroy()
+        app.quit()
 
-    # window close event
     def closeEvent(self, event):
-        self.appIndicatorHide()
-
+        """window close event"""
+        event.ignore()
         trayonclose = BMConfigParser().safeGetBoolean(
             'bitmessagesettings', 'trayonclose')
-
-        event.ignore()
-        if not trayonclose:
-            # quit the application
+        if trayonclose:
+            self.appIndicatorHide()
+        else:
+            # custom quit method
             self.quit()
 
     def on_action_InboxMessageForceHtml(self):
@@ -3659,4 +3661,4 @@ def run():
     if not BMConfigParser().getboolean('bitmessagesettings', 'startintray'):
         myapp.show()
 
-    sys.exit(app.exec_())
+    app.exec_()