It's April 6, 2016. Now with Prestashop 1.6.1.4 and I have the same issue. I set up combinations in the product page, then set up specific prices for discounts. Prices display correctly on product pages, but become $0 when added to cart. I have searched and searched, and cannot find a solution. "Problem with "default bootstrap" template" is the closest to an answer.
Is there no solution?