We are using calculated shipping method: UPS. We are offering both physical and downloadable products.
When you go to check out with a downloadable product, all the shipping options have prices; this should not be the case. I do not see a setting in the product or the store shipping settings to resolve this.
Example here: http://store.legalnursenetwork.com/store/products/laplink-pc-mover-professional-8/
Just add to cart and continue to checkout.