I can empathize with you. My daughter is 3 1/2 and has a similar history. She was diagnosed with asthma at 18 months, but I feel that as of the last 3/4 of a year, it is something different. The coughing is more from the throat and on expiration. I kept trying to tell the various doctors this (along with the fact that she was not wheezing) who treated her when she was in distress. I also tried to explain this to the pulmonogist that she sees. His reply was to load her up on more steroids. Now, I have a daughter who acts like she has ADHD. So, I got fed up, started weaning her off of the steroids, and went to see a homeopath. She was doing pretty good until I tried to take her off of the last 1 mg pulmicort/day. She had a major coughing attack. (I should have weaned her off more slowly)
So, I made a appointment with her pediatrician the day after just to talk. I had also read on the internet that GERD could cause nighttime coughing. In my daughter's case, I also wonder about some sort of tracheal narrowing. Anyways, her pediatrician was great, listened to all of my concerns and descriptions, and contacted the pulmonologist to schedule a bronchoscopy to try to visualize signs of any kind of congenital trachea problems, or signs of GERD.
Hang in there! Observe everything and write it down...you are the one that is with your child the most, you can describe all of the conditions that help lead up to a coughing fit...that will help them a lot.
Good Luck!
I have a couple of ideas. Since the coughing is worse at night than the daytime we should look at the difference between the situations. That is at night he is lying down and during the day he is standing up or sitting. This suggests that perhaps gastric fluid is seeping up and going back down his trachea, precipitating an asthmatic attack. It also suggests his LES (Lower esophageal sphincter) is not closing properly.
As we know a virus doesn't respond to antibiotics. I am sure there is a misunderstanding between you and your physician.
I believe his problems are not being paid proper attention to. I also suspect there is a communications gap between you and his pediatrician. I am not saying the doctor is incompetent.
You should arrange for along sit-down with this pediatrician, and if he doesn't agree to that find another medical professional.
Nothing bothers me more than a child in discomfort.
There are medications available to break up phlegm and you should consult with your physician as to which ones he feels are appropriate.