Normally the flapper floats until the tank is empty. Then it "falls" shut. Either: 1) the tank is failing to empty completely for some reason or 2) the flapper falls but doesn't stay down when the water starts to fill on top of it. I believe the thing that makes it stay down is vacuum. If it was working OK and this is a new problem, then I'd say there's a problem elsewhere in your system. Anything changed lately in your house? If you've just made some changes to this commode, could it be that the water filling the tank is coming into the tank in such a way that it is lifting the flapper at one edge, breaking the seal? If that's the case, you might need to adjust how the water is entering the tank. Also, make sure that the flapper is sealing properly when the tank is empty.

That may very well solve your problem if you have high water pressure.The water rushing in holds the flapper open.This is also the reason you hear of a clogged toilet which continues to overflow.The water takes a direct path past the flapper,to the bowl,to the floor and will continue until shut-off.

Is the tank tilted to one side? When the flap is down, the weight of the water above helps seal. If tilted, the flap may float before the water pins it down.