I have a 1 year old who I believe went through the same thing...even though her reflux test came back negative, and the ear, nose and throat specialist said there was nothing to be concerned about.
Her breathing was very labored, especially at night while she was on her back. She was breastfed for 2 months...then i switched to Alimentum Similac and her reflux virtually disappeared in about a week, but she immediately slept better from the first bottle. it was incredible...and her labored breathing was gone shortly after that. i would suggest Similac Alimnetum to anyone with a child who has reflux. it is more $$ but sooooo worth it!!!!!!!!!!!!