Murphy was the same when he was a puppy. We didn't know better so ended up constantly changing his food, hand feeding, making a huge fuss of him to get him to eat. Then we were told about the 15 minute rule. He soon learned if he didn't eat he didn't get anything else. Remember not to feed treats in between meals if Charlie isn't eating.
One other thing is most makers recommend huge portions in both adult and puppy feeding guides, I find my two do fine on half the makers recommended feeding guide. So just make sure your not filling him up in one big meal, making him too full for the next one. Maybe try feeding him less to see if he's simply too full?
Paula - mum to Murphy(6) & Misty(7), and Jerry our cat.