He's still angry with her too, for being swallowed up by the Eye of Harmony. That incident might have had much to do with his brutal treatment of her. The Master is truing to asses what this human form can do. If she has the same kind of power in this body... he doesn't care to contemplate what she might be able to inflict on him.

"You keep away from me," he hisses at her. The Master doesn't need to ask. He knows what raw, untamed power is harnessed by a TARDIS.