I would ask him about it. "I see you didn't eat your lunch today... you weren't hungry?... (long pause..)" see what he says. Is the packaging difficult for him to open on his own? I would also suggest talking directly to his "teacher" out of his earshot. Is she aware of this? What have they tried? Do other kids do this? Does she notice anything different from snacktime to lunchtime? Does he seem sad then?
I don't know the answer, but I'd start asking questions... Maybe you could put sticky notes on the different portions in his lunch... draw smiley faces on each one, or hearts signifying "I love you" or something... Is the food stuff he likes? My 6 yr old daughter loves PB & J but refuses to eat them if the bread gets the least bit crusty on the outside... Is there some ritual you do at home that he is missing at the meal at daycare?
Maybe someone else has been through this and has suggestions. My daughter does this sort of thing sometimes, but she is much older and KNOWS what she is doing....