C.H.
I would call the doc again and explain what's going on. Your son may have a lactose intolerance - maybe the lactose in the breastmilk was so low that he didn't get enough to bother him. They should be able to offer help. I'm not sure how old your son it (I'm assuming he's turning 1?), but an option to ask the doc about is the 2nd step formulas. They have formulas now that are made for 9 through (I think) 24 months.
Good luck - I hope you get some good advice!!