Did the old flapper seem to hook up to a pair of hooks so it hinge up and down? like the pic below
If so lots of people make the mistake of buying the universal flapper that has a round ring in the middle to be used on the old lift wire Douglas valve and they seem to slide the rubber part around the overflow tube on the hook type which will not allow it to seat properly. So if your flush valve body has the hooks ensure that you remove the round ring part and hook it on properly. The next [picture is of a flush valve with out the hooks.
Oh I also recommend if you bought a fluidmaster flapper or a no name one return it. By a Korky Flapper. Just remember that ring in the middle needs to be removed before using the hooks.