My ears have been popping a lot?

For the past month I have had a congested and my ears have been popping, and I also have had a cough. I went to my normal doctor awhile back and he said it was allergies and told me to take Claritin. I took that for several weeks and several days ago I was still experiencing the same problems. I even woke up with throbbing pain in my right ear, which made my head hurt. So I went to the doctors again, this time the first one I could go to. He checked my ears out and my nose and said I had a sinus infection and an ear infection. He prescribed me amoxicillin 875 mg and told me to take Musinex D for my cough. The Amoxicillin is helping but my ears are popping still? What if I finish the course of Amoxicillin and my ears are still popping, what could be the problem with my ears?