Python autoclicker doesn't work on another window

Question

here's my problem : I made an autoclicker to automate some stuffs and it perfectly work on app like Opera or just my os. But I want it to work on a special app "Wabbajack", and when I have this app in foreground, my script doesn't work anymore : nothing happen like a freeze during i'm on this app. Do you know how i can fix this issue ?

PS : it is probably a security from the app but don't worry i'm not cheating, stealing or do anything who would be illegal, i'm just trying to automate a boring installation

Here's my code

import time
import threading
from pynput.mouse import Button, Controller
from pynput.keyboard import Listener, KeyCode


start_stop_key = KeyCode(char='s')
exit_key = KeyCode(char='e')
position_vortex0 = (1080, 620)
position_vortex1 = (1080, 655)
position_vortex2 = (1080, 690)


class ClickMouse(threading.Thread):
    def __init__(self):
        super(ClickMouse, self).__init__()
        self.short_delay = 1
        self.delay = 4
        self.button = Button.left
        self.running = False
        self.program_running = True

    def start_clicking(self):
        self.running = True

    def stop_clicking(self):
        self.running = False

    def exit(self):
        self.stop_clicking()
        self.program_running = False

    def click(self, position):
        mouse.position = position
        time.sleep(0.2)
        mouse.click(self.button)
        time.sleep(self.short_delay)

    def run(self):
        while self.program_running:
            while self.running:
                self.click(position_vortex0)
                self.click(position_vortex1)
                self.click(position_vortex2)
            time.sleep(0.1)


mouse = Controller()
click_thread = ClickMouse()
click_thread.start()


def on_press(key):
    if key == start_stop_key:
        if click_thread.running:
            click_thread.stop_clicking()
        else:
            click_thread.start_clicking()
    elif key == exit_key:
        click_thread.exit()
        listener.stop()


with Listener(on_press=on_press) as listener:
    listener.join()

This code is suppose to click on installation button who appear at random time. It perfectly work on others app and just click on 3 position before loop at "while self.running" who is True when I press "s"