What you are describing sounds like aspiration, and is not a very good symptom to have. I would recommend that you follow up with your GI doctor. My mom had severe reflux, and she used to have this problem. The danger is that the acid can travel down your windpipe while and can literally choke you to death. My mom was advised to sleep with her head majorly elevated--she slept sitting straight up at one time. I've also had this symptom before, especially when I was pregnant. After I had my babies, my doctor started me on REglan. This drug closed my LES (lower esophagael sphincter) so that acid could not travel up my esophagus at all. Combined with PPI's and acid blockers, my symptoms are rather well-controlled.