Hi Sandy,
That is the expected behaviour with one instance. The settings shortcode moves the search settings for the given search instance. In your case the settings was moved to the pop-up content. Since the pop-up is not visible after closing, the settings are not visible either.
I tried to test two instances to see what exactly happens, but I am getting the following error when visiting your site: https://i.imgur.com/HTaRRUp.png
