Hi J., we discovered my daughter had reflux also in her 1st year of life and she too was on meds. Have you gone to a Peds GI doc yet? They will be able to help give more answers to what's really going on and can do an endoscopy to see what is really going on in his throat and stomach; or whatever ever other testing they might see fit.
Have you also considered that it's allergies? It's that time of year and I know that allergies affect my throat and it gets scratchy and I have to constantly clear my throat and/or cough. One may think it's a cold, but it's not. Claritin works for me and clears it all up. You might want to get him tested for allergies or speak to his pediatrician about the possibility and see if he can take over the counter allergy medicine and see if that will work.
Good luck to you! I went through a whole year ordeal with my daughter and this stuff and it's exhausting and frustrating as a parent! I hope that you find some answers, but follow your gut instinct and push for whatever you feel is right for your child!