the little rubber seal outside is for "decoration" purpose only, the actual seal is a silicone liquid gasket that is applied to the screen and then the screen is placed onto the car, The leak is in the sealant which they missed at some points, to remedy this, the windshield requires rebonding to the car.
This time - do not use any generic rtv, get the real Honda stuff from the dealer - it should be a threebond product, along with the correct cleaner and activator. - Once the glass is in place make sure to not drive the car for atleast 6 hours to prevent the glass moving and tearing its liquid seal.