What's his cry like? Is it an all out cry to get you, or is he just fussing like maybe he doesn't want to be awake and is trying to settle himself back down? Are you going in there right away or do you give him sometime to get back to sleep? When you are putting him down at night are you leaving him still awake, even though you are helping him to get to a very sleepy phase with the hand on his bum? Also... is this something that has been going on for a while or is happening with cutting teeth or something along those lines?
Kyra does this thing occasionally where she cries really loudly all of a sudden. I realized that by rushing in there too quickly I was actually waking her up. Now, I make sure that I got to the bathroom before I go check on her. Those few minutes allow her to settle down 95% of the time. When I peek in on her (I do so without being noticed) she is back to sleep or already settling and snuggling blankie to get back to sleep. It really bothered me for a while. I wanted an explanation for those outbursts. My doctor just said that there really isn't one and if she is settling back to sleep not to worry. When she isn't settling at that point... she is really awake and something is usually wrong.