We had a doctor watch us breast feed and talked with 2 lactation consultants and everyone thinks the problem is reflux.
The good news is that their digestive systems eventually mature so it's only a temporary problem. It's also great that he's gaining weight and we have plenty of milk. We put him on some medicine and it seems to be helping. Now instead of having 1 or 2 good feedings a day we have 1 or 2 fussy feeding a day. We're going to give it a few weeks and then try stopping it and see if there is a difference. I hate putting him on meds but the other option was to stop breastfeeding and I'm not one to give up on things. This is where I can use my stubbornness for good.