Please keep us posted as I am curcious as to what happens as I am dealing with the same problem.
My son since about 2 weeks old always arched his back, screamed in pain, never slept. They said he had colic and gave him a hypoallergenic formula (normally used for infants with an intolerance to milk).
Anyhow from day one I thought it was reflux, but No who was I was, just his mommy..
Now at 6 months old, and after changing doctors, he has been dignosed with acid reflux. Personally that is what is sounds like to me. If it was a milk intolerance, that normally takes about an hour after eating to show signs. If within 15 / 30 minutes after eating it is normally reflux.
I hope things get better for you on the medicine, we are finally on medicine also so we will see!
Good Luck