I was a healthy-looking baby. I would eat the normal CF amount every day. My parents fed me whenever I seemed hungry. And yet, every night I woke up screaming. They didn't have a clue what was wrong, they tried burping me and walking me up the street and taking me for a drive, etc etc. Finally one night they tried feeding me, even though they were sure I had been eating enough. I gobbled it down like I was starving, and went right back to sleep.
Try feeding him again, even if it seems unreasonable to you. CFers are little piggies, if you're lucky.
Other than that... I say reflux is a real possibility. And beyond that, maybe gas. Gas can be surprisingly painful sometimes.