1. On your demo website, you don't use the effects on the main menu. And that menu effect, which is made by your template, is the one loading all the javascript causing the problem with the popup system.
2. Well, as I said, you could change that you make it more obvious.
Alternatively, you could also change the option "After a product is added to the cart" of the configuration in order to display a popup so that the user has the possibility to go to the checkout when he clicks on the add to cart button.