Our (now 4 year old) had the same issue. It manifested itself when my wife was breast feeding. She found that if she drank milk, then the baby was very fussy. She switched to soy milk and, just like that it helped.
So when she quit breast feeding what did we do?? Started the baby on milk based formula!! You'd think that 2 college educated people would have known to use soy based, but we must have had brain lock.. after a couple of weeks we finally figured it out and switched, and again the fussiness turned off like a light switch.
All kids are different, but that was our experience.
hens