It could be something to do with the threads themselves, and no matter what is done, it just wont cure it, but when shooting a couple of rounds, it forces the threads to seat, and the resonance is stopped. The only thing one might try, at first, would be to clamp an extra weight of some sort, close to the brake, and shoot it, to see what happens. It might be just something like removing a little metal, somewhere on the break, and it would stop it from doing it, like spin balancing something. That is, if this is what is causing it.
If it did it every shot, I would think of something like the ports causing the gas to change or swirl behind the bullet somehow, and make the bullet travel abnormally. But this only happens for two shots.
Things like resonance and barrel whip are funny things to work with, since you can't really see it, and can be a pain to get rid of, if a barrel, or extension of it, has a problem.