My 3 month old daughter has a bad cough/congestion and is wheezing?

she has had this problem since birth and has been hospitalized twice for a week at a time for it. She occasionally stops breathing and her heartrate decelerates because of it. they have diagnosed her with bad acid reflux (GERD) and say this is the cause. My concern is that on top of this she is always seeming to get sick. She is breastfed which should help her not get as many colds but she seems to catch one once every 2-3 weeks. She is always veeeery congested and has a horrible cough. She is taking prilosec and reglan and uses a nebulizer and she still has these problems. My question is, am I missing something? Has anyone experienced the same thing with their baby? It just seems like maybe there's an underlying condition that I'm not thinking of. Anybody have any suggestions? Thank you in advance