I know this is a old thread but this solution can help other people.
Recently one of our customers has also this problem. The customer of that particular webshop orders a product, selected a billing address and clicks the button "Continue" and there is the pop-up "Your cart is empty".
You can solve / prevent this problem to make sure your URL's (www and non www) always resolve to the same URL as configured in the store settings.
For example, if your store in nopCommerce is configured with http://www.myshop.nl. Make sure you select "Pages should have WWW prefix" in de SEO settings or create a IIS URL rewrite to rewrite all URL's to the www version of the site.