I have the same problem but it isnt the water level... I even increased that to the max. I have one of the water saving ones :(
The problem is that the flapper valve closes too early. It has a flapper of the type with a cylinder that the water drains out of as well as another closed cylinder that acts as a bob I guess. Well, after about half of the cylinder of water empties, the flapper closes, before all the water has emptied. How to fix..?
1. buy a new flapper valve of a different type? It appears that the hinge is about 3/4-1" above the bottom of the tank so that contributes to the problem... I dunno if I can find one that is compatible but is a different design?
2. try and close off the hole somewhat that empties the water from the cylinder so that it empties slower, trying to time it so that it empties once the tank is empty.