I'm sorry to hear that your baby is sick. There are cases of babies getting Inflammatory Bowel Disease, but of course it is rare. I'm wondering if the food at night is bothering his stomach since he doesnt seem to become relaxed with a full tummy. However I am not with him, and if he seems hungry then he's probably hungry. I would ask your pediatrician about seeing a GI because it can't hurt to get a second opinion especially from a specialist.
Diagnosed: 2003, age 18 (had issues with it since I was 12)
Meds for crohns: Remicade every 6 weeks, 6-mp, Nexium (GERD)
Other medical issues: Hereditary Spherocytosis (hemolytic anemia) iron deficient anemia, polyarthralgia, ovarian cysts, Migraines, GERD
Surgeries: Spleen, Gallbladder, Tonsils, Adenoids, foot of terminal Ileum, Appendix, Ileocecal valve, bit of colon