You are correct about the pocket on the bottom of the flapper, it has air under it after a flush. When you lift, the air is trapped until the water level drops, allowing it to return to it's seat.
What you were told about the flapper needing to settle in is often the case. There is a little biology usually involved though.
If you've noticed in most tanks there is some mix of sediment, calcification and scum. Scummy slime is what your flapper is likely missing.
After a long period, water in the tank begins to get a bit of algae growth in it. Everything gets a slimy coating. This generally acts as a lubricant and to some degree a seal. Even in municipal water which is chlorinated there will be this buildup. eventually.
Your new flapper lacks this. The WD-40 idea goes the right way but is the wrong product since it is WD or "water displacing".
If your still dealing with this, try the following.
Get some petroleum jelly (some have also used shortening such as Crisco or even ham fat)
Turn off the tank supply valve
Flush the water out of the tank
Lift the flapper and put a light film of petroleum around the rubber on the flap and where it seats
Lower the flapper down and push a little to spread the petroleum between the flapper and its seat.
Open the flapper using the lever on the tank a few times. If its tight, as in not wanting to open, you've put too much jelly on. Lift flap and remove some, making it thinner.
Turn the supply line back on and let the tank fill, then try flushing again.
One problem can be some end play at the sides of the hinge where the flapper swings, if it slides sideways too much this can cause hanging. This can be tricky to fix.
There shouldn't be this problem with new hardware but not all are created equal. You can put a little dab of jell there also. The weight of the flapper should recenter it.
Another problem can be the lift chain/connector. If it seems it is getting link locked, that is the links are not floating down free causing the flapper to not go down consistantly, remove the chain and replace with heavy (20 to 30lb) monofilament fishing line or 550 multistrand cord. If you do this, you'll need to assure the end connected at the bottom does not bind in up or down position.
What an adventure huh? Particularly fun at 2 AM isn't it? Not to mention lost water.
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