It is possible that you are the victim of a crossup. That is, his attack comes out at a time where he passes through you and his attack counts as coming from behind you instead of in front of you. Therefore the game thinks you are blocking in the wrong direction and you take full damage.
I am not sure how you would prevent this other than to maintain a certain spacing from him (about a foot away from him?) so that, when he uses this attack string, you are not at that bad position when his second attack comes at you.
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