thank you for your reply and desire to fix this. As this is a public site, I am uncomfortable putting this information online.
Having said that I am sure that it might have to do with the plugin incorrectly sensing popup blocker as turned on. I tried another plugin (which was actually working) and turned on the popup blocker on chrome and it did exactly the same thing – window appeared briefly and they quickly vanished. Problem with your plugin was that it was doing this even though the popup blocker was turned off (I kept testing by turning on and off). It did work on Firefox but not on Safari or Chrome. Also, it might have to do with customization to the checkout page. Regardless, other apps are working.