Toto Flapper not Closing

I have just replaced the flapper on a three year old Toto single piece low back toilet gravity flush toilet. Chlorine apparently disfigured the old one and the toilet would run for a bit after filling the tank leaving the bowl with a indeterminate water level, always lower than where it should be, and slowly running/filling off and on after the flush.

Unfortunately after replacing the flapper with the proper part from Toto, I have the same problem. The tank fills, stops then fills slightly on and off until the flapper seals. If I push down on the flapper to seal it stops running. This problem doesn't seem to matter how the chain is adjusted.

How do I fix this? I have thought about solvents to make the flapper a bit more pliable but am at a loss. Any help/advice is greatly appreciated.

-mg

Silicone spray is sometimes used on flappersi to make them seal better.
Korky makes replacement flappers for Toto, I find them at Lowes next to the Korky Quietfill valve.