Is your pause menu set as autoload? The easiest thing would be to not autoload it and just add an instance of the pause scene to any scenes you do want it to operate in.
If you really want it to autoload you could have a boolean in your pause menu which is set on _ready function of each scene loaded to true or false depending on if the pause should operate there or not then change the pause menu code like
func process(delta):
if NewBoolean and Input.isactionpressed("ESC"):
visible = true
gettree().paused = true
You can make your escape key function as a pause and unpause:
func _process(delta):
if not Input.is_action_just_pressed("ESC"):
return # do nothing if escape isn't pressed
elif visible: # we are paused
visible = false
get_tree().paused = false
else: # we are unpaused
visible = true
get_tree().paused = true