It sounds very much to me that he is being picky about what he eats. You should be the one who determines what he eats and not visa versa. As long as you are giving him a healthy food without fillers and it meets requirements he should be fine. If he will eat chicken and treats then there is nothing wrong with his digestive track.
At his age he should be eating 2-3 cups of a nutritional meal a day. Try putting a cup of food in his bowl in the morning. Give him 10-15 minutes to eat it. If he doesn't eat it pick the bowl up and let him go without eating anything else (like snacks or people food). At lunch time, or when you get home from work, put one cup of food in the bowl and see if he eats it. If not pick it up and try the same thing at dinner time. Repeat as needed but don't give in and feed him something else. Remember that a healthy dog will not starve itself. What you are establishing here is that when you put the food down it is time to eat and more importantly, if you don't eat what I feed you, you don't eat.
This is not cruel or being mean, it is training the dog. Usually the dog will eat within a couple days. As I said, if you pick a healthy food, he will be fine. To answer your last question, it is not so much that he doesn't like the food you are giving him as much as he likes the chicken better and is training you to feed him that.
Best of luck, let us know how things work out.