Right, that’s because the Script Action was being ignored while using the Navigate Action. Moving to the Script Action with a navigation method will suffice as a workaround for now as the Script Action will now appropriately set the desired variables.
Side note:
If your Navigation View will always set the Session variables onStartup, you don’t need to set them before navigating to it, and you actually shouldn’t set them before navigating, as it will only make your personal debugging more difficult.