put a couple of drops of food coloring in the tank and see if the color leaches into the bowl. If so, it still has to be the flapper. Sometimes a new flapper will not work, sometimes the hole that the flapper covers needs some rounding work done do make a good seal. Check for mineral deposits on the hole's lip.
It really has only two places to go, over the spill pipe and leaking under the flapper.
Is the chain too tight as to not allow a proper seat?