You can contact the plugin developer. The guy is awesome for help. I understand I had the same issue. Set it up like this:
1. Don't have a shipping class for the item.
2. Use Advanced Shipping Pricing option Down load the extension from the plugin if you have not yet done so.
3. Set you price for the product to 0.00
4. At the bottom, go to Advanced Pricing and select product. Ad in Minimum 1 item and the price for shipping.
Test by adding the item to cart and checkout.