Simplest explanation I can think of: there's no reason to model this event as if all of its energy is emitted from a point source. As the NYT article put it, the size of the explosion is comparable to the orbit of Neptune. Meanwhile, two seconds at the speed of light is less than the orbit of Earth's moon.

So, if the gravitational effects originate from the center of mass of the explosion, and the gamma rays originate from some kind of Big Bang-like recombination phenomenon happening a few hundred million km away from the center of the expanding shell, that would easily account for the difference.