Hoo boy, does this sound like me!!!
Hi Nathan, I'm Janice. I have GERD, LPR, Vocal Cord Dysfunction, Bronchiolitis caused by aspirating the acid from my stomach, etc. I had heartburn for years, but never that bad, I did, however, have an asthma like condition that could never be specifically diagnosed.
For years I had flares of pulmonary issues, each time getting longer and worse. I had so much trouble breathing and then suddenly I would get better. I lost my voice all the time, I coughed, I cleared my throat..on and on. My asthma/allergist Dr. did a scope of sorts and found "cobblestoning" in my throat and diagnosed LPR, my other A/A Dr suspected Vocal Cord Dysfunction, but no way to prove it. The pulmonary guys in my town were ineffective and unable to think outside of the typical COPD, Emphysema, asthma stuff so they couldn't deal with me. My a/a Dr put me on Protonix twice a day (I was already on it once a day).
Before I go on, yes, it is unusual for the med to take this long to work...Nexium may not be a good fit for you; I went through all 4 PPI's before finding that Protonix was the right one...
So, on with my story. Eventually, my Dr.'s sent me to National Jewish Hospital in Denver to find out why my breathing and other issues were getting so much worse. Among other things they found my reflux was very serious. When I came home and back to my gastroenterologist and family Dr. they decided to send me to Cleveland Clinic. After testing they determined that I was bad enough and a good surgical candidate for a Nissen.
I had the surgery on July 16th...no picnic, but I am getting better.. I have no more hoarseness, coughing, throat clearing. My lungs are permanently damaged, but now that the valve is repaired the acid is no longer getting in there to burn them and damage them any further.
So, the short answer to a very long story, is that yes, the acid could very easily be the culprit behind what you are experiencing and the nexium does not seem to be a good fit for you.