C.C.
I would schedule an appointment with the pediatrician and just make sure nothing is wrong (ear infection, food allergies, who knows what).
If nothing is physically wrong, then just make sure you are keeping him on a very consistent schedule. In bed by 6pm (yes, really), naptimes right on schedule every afternoon, and very consistent meal times.
The other thing I'm thinking is that maybe it could be nightmares, or even night frights. One of my girls would look like she was wide awake, and would scream and cry, but she was dead asleep. It was the freakiest thing. It started around 18 months for her, and went on for several months. For instance, she'd get out of bed (she was in a toddler bed because she was an escape artist), she'd come and wake me up crying and tell me there were grasshoppers in her bed. I'd go with her to look, and she would point and cry, and of course there were no grasshoppers in her bed! Anyway, she was literally seeing them there. So I would "smash" the grasshoppers, put her back in bed, and she would be asleep (actually close her eyes) and be completely asleep in 10 seconds. It was the weirdest thing. She did grow out of it. But maybe your son is having that kind of thing happen, where he's not REALLY awake, just looks that way.
Anyhow, frustrating issue. Maybe other moms will have some good ideas. Good luck with it. =(