Even more recently, I had a second toilet that was intermittently running on its own. I replaced that seal, and the same bump was there on that seal! The replacement valve seals do not have any bumps (as I would expect). Is this bump expected on some seals? Or does this happen over time for some reason?
If you take seal out of water for a day, you'll notice the bump's swelling will go down (not a manufactured feature of the seal). Not sure if the dimple is result of manufacturer's defect, or if it just happens to all these type of seals over time. The bump is indeed the cause of your leak. I've had dimples like this twice on my Kohler canister-flush toilets. Could be the unique chemistry of the water where we live.
The bump/dimple develops over time, and is indeed the reason why your toilet is running. I've had this problem occur more than once, with the same dimple on aged gaskets. In my case, I need to use chlorine tablets given the inherent cultures in the air where I live (to keep the toilet from growing black gunk). I know it's against the manufacturer's rec, but it's a payoff not having the mold grow in my toilet (cleaning the toilet regularly with bleach/Pine-Sol still doesn't arrest the black gunk). So, in my case, I assume it's the bleach tablet that causes the compromised dimple, and I live with that, replacing them about once a year to keep the toilet from running.
I was gone for 4 months and when I returned, I received a water bill of over $200 because of this defective "dimple" in the flapper gasket. My usage went from 2 units of water to over 17!
I discovered that over time the gasket absorbs water between the two layers of neoprene and caused these bumps or dimples to form. My gasket had them on both sides and not necessarily opposite each other.
I removed the gasket from the flapper and took a utility knife, cut just deep enough to pierce one layer and water came out! I pressed on the gasket and all the water came out. The dimples disappeared and so far, the toilet is not leaking water around the flapper.
A design defect in my opinion!
I think it is a design feature in the gasket. I have had to replace several gaskets over this last year. Due to a bump developing in the gasket. The new gaskets have no bump. The gaskets are not too expensive but that and the additional cost in the water bill add up! It would be nice to find out what is causing the bump to appear - research by the company is needed. Apparently this is an on-going problem with this type of gasket.