It is my understanding that you can have reflux without actually feeling the "heartburn". I have full gerds, and lpr. When I first started noticing problems, and was diagnosed with gerds, I was having alot of heartburn. Now, I dont have the heartburn as much, but I am struggling alot with lpr which for me atleast, has some different symptoms than heartburn. But, it is the same in that it has acid that comes up and sits in my throat area. In either case, its the acid producing the problems. Also, being that your son is only 2 years old, is it possible that he never was fully able to communicate to you that he was having digestive problems? Plus, if this is all hes known for so long, he may not have realized that it was not "normal".
In any event, I wish you the best of luck! Please keep us posted....