How can I determine why my toilets are not flushing right?
To my knowledge most newer toilets manufactured after the water saving regulations were put in place do not completely empty the tank when they flush. The extra water is there to provide extra height to the water which increases the water pressure as it flows into the bowl. 

If your toilet's flushing performance is fine then leave it as is. If not replace the flapper with an adjustable flapper. This can either be a flapper with a dial or a flapper with a float on the chain (you can even get the floats separately to add to your existing flapper chain). These help control how long the flapper stays open after you flush.