Just a couple points - make sure the new flapper is adjusted properly. if it is too close to the flow of water, it gets sucked back into place. It needs to be situated high enough that it can just close and seal. Any farther and it won't seal, any closer and it seals too quickly.
Also, as already mentioned, the chain should be short enough that it pulls the flapper all the way up and perpendicular to the bottom of the tank.
Finally, while most flappers should work in just about all tanks, sometimes one will work better that another. If you are confident the instalalton and adjustment are correct, then trying another style might solve the problem.
- It's not rocket science...unless of course you are working on rockets, then it is. -