Hi - like the others have said, it could be reflux issues. We had a similar situation with our little boy when he was 5 months old, and finally the clinic took me seriously and put him on Reglen and Prevacid and things have improved with the reflux symptons.
Tom's lungs also sounded clear, but after some expert advice from the others on this site I insisted on a x-ray and it did infact show that he had some mucus plugs - they thought pneumonia at first and hospitalised him, but as he was showing no real symptons they ordered another x-ray before they did the bronch and he was downgraded to bronchitis and sent home, and no bronch. But the throat culture they did showed he had a psuedonomia infection so he was switched to Cipro and started on TOBI and has been perfect ever since - he is now almost 7 months.
My long winded point here is, you have to be persistent and trust your MOM instincts - we know our babies better than anyone. Just keep pushing until you are satisfied with the answers. If he had a throat swab - like you say, it is great news that he is not showing anything! Although, as I have been told a throat swab is not always accurate as bacteria in lungs cannot always be detected by a throat swab - a bronch is best, but my clinic decided it was not necessary at such a young age without severe lung symptons.
Tom is now on Pulmozyme, Abuterol and Pulmicort and his cough is no longer. Good luck with everything! PM if you need to chat, I know just how confusing and worrying all of this can be - hang in there!
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Natalie, Mom to Tom, w/cf 7 months DDF508 and Jack, 3 no cf