Few, if any, modern toilets since the mandated low-flow requirements, flush the entire tank during a normal cycle - they use the height of the water to provide more oomph for the flush. To accomplish this, they design their flapper to only stay up a certain amount of time. A universal replacement is unlikely to have that calibration, and will stay up longer, letting more water out. Enough water will cause it to do what you've seen. An adjustable flapper or an OEM, or one made specifically for your toilet as an aftermarket is the only way to drop the water use to the mandated amount. Using the wrong flapper, or incorrectly adjusting an adjustable one could use as much as twice the water mandated, and is a really bad thing in SoCal where water is especially dear.