This is my experience: My daughter was diagnosed with silent acid reflux when and infant (4 months). We put her on Zantac and it did a little bit to control it, but she still had some trouble. She then learned to spit it out after a couple of months. It tasted awful.
We then went to Prevacid and it helped a little bit better, but still not enough. She was on Prevacid until just after a year old. I wasn't seeing a lot of improvement and the doctor expected her to stop having trouble at a year. Well, not my daughter. I finally took her to a Naturopath and she put her on Bifidous powder 1/2 tsp and Glutamine (don't remember the dose). WOW, instant improvement. Oh, I took her off prescriptions at that point, too.
After about 6 months of the combo Bifidous and Glutamine, we took her off of the Glutamine and she continued the Bifidous. She continued to be better.
With my son, it wasn't so silent and the Naturopath put him on Bifidous at 2 weeks old. He had problems from the very beginning. We saw vast improvement with gas buildup and spitting up after he started the Bifidous.
I still give both kids a probiotic at night just to keep everything on even keel.
You should take your son to a Naturopath if your insurance will pay for it. If not, try adding in a probiotic that is more formulated to small children, like Bifidous or Primadophilous. I can get Primadophilous at Fred Meyer in the natural foods section - refridgerated case. I'm in Tigard, so close by if you have any more questions. I can recommend a Naturopath that specializes in kids, in Beaverton, if you would like. Just contact me and I'll pass on whatever info. you need.