Actually, free shipping gives sellers automatic 5 in the shipping star, however, most sellers will ship via the slowest method for free. When charging the actual shipping cost, not even the handling fee, sellers may still suffer, because some buyers will ding their shipping star because they may feel that shipping should have been for free or may get mad at something else and dings a shipping star for no real reason.As of to low shipping charges, some sellers made it this way instead of give free shipping. I think I read in here a seller wrote that her star is higher for shipping and handling when she lower the shipping charges, instead of give free shipping. Her thought was that her customers feels she is generous in lower the actual cost if shipping, while if give free shipping, customer think that she put the price of the item higher to cover the "free" shipping.
And I absolutely agree, way to early too file claim of anything especially non performing seller.
So OP I think you should not worry about the too low shipping charges, it is not your problem.
Some sellers care about the stars, because that effects their TRS and therefore fee discount, but some don't care about jumping through numerous Ebay hoops in order to keep their discount.