Maybe the first time got sick on it has left an impression on his brain. He associates mac & cheese with getting sick, so that's what happens when he eats it. Our minds are VERY powerful things! I'm 32 years old and to this day I can't take Pepto or drink red Gatorade. I had the horrible flu when I was a kid and that's how my aunt treated it. Not that she did wrong or anything, but now I will forever associate Pepto and red Gatorade with throwing up. I tried a little Pepto about 2 years ago. It hit my stomach and came right back up. If I even smell red Gatorade, I start gagging.
Since he doesn't have any type of reaction to the stuff in the mac and cheese unless it's actual Mac and Cheese, I just wouldn't give it to him. If you really want him to have it, try a different kind. If you're using the stuff with the powder, try the stuff with the creamy cheese or make your own.