I did not say that he lost control of it in so many words. In fact, until recently I believe it was not in his interest to stop the black Grail's actions, assuming he did have the capacity to. Zouken himself was killed and his Assassin neutralized while pursuing Illyasviel, though I am not sure what is to happen after that.

[or, 'he was controlling it and now he's dead']

While my memories fail me as to the specifics, I believe it has been doing exactly that.