Not only but also Naipaul

In V. S. Naipaul’s novel Half a Life, a boy is waging a battle, mostly silent, with his father, through stories he writes and leaves lying around strategically at home. One day the boy, Willie, is home from school for lunch and sees his exercise book still untouched.

Willie thought in his head, in English, “He is not only a fraud, but a coward.” The sentence didn’t sound right; there was a break in the logic somewhere. So he did it over. “Not only is he a fraud, but he is also a coward.” The inversion in the beginning of the sentence worried him, and the “but” seemed odd, and the “also.” And then, on the way back to the Canadian mission school, the grammatical fussiness of his composition class took over. He tried out other versions of the sentence in his head, and he found when he got to the school that he had forgotten his father and the occasion.

This passage, even apart from cultural, familial, and psychological complications, is interesting from the point of view of grammar and style. I’m curious about what ‘didn’t sound right’ to Willie in the first formulation of the line. What ‘break in the logic’ does he feel?