I have it where when you click on the menu it starts the game, but after that every time you click I puts you back at the beginning of the game
A link to your project, script and other useful information with screenshots will be nice.
ok try clicking after the menu and it resets
Can you try to add the code below before you change the scene?
this.app.mouse.off(pc.EVENT_MOUSEDOWN, this.onMouseDown, this);
In your case you can also use
this.app.mouse.once instead of
this.app.mouse.on in your initialize function.