3 year old still sick after 6 weeks and 2 rounds of antibiotics!

My 3 1/2 year old and my 8 month old came down with chest colds with a runny nose and nasty cough over 6 weeks ago. Had a fever for a few days and then started to get a little better around 2 weeks. But after 4 weeks they were not back to normal and were starting to get worse again, lost of coughing and fever. I took them to the Dr. and they said my 3 year old had a sinus infections and the baby had an ear infection and bronchial infection. They both went on Amoxicillin. Baby just finished his meds and is good so far. My 3 year old had a reaction to the meds after 8 days so was switched to Zithromax. Tomorrow is his last dose and today he woke up with a fever. About 100.5, not too high, but he is coughing more and seems, I think, too sick for a kid who has been on 12 days of antibiotics! I called the Pediatrician and the nurse says he may just need another round of the Z Pack, I should see how he is in a couple days and call if he is still sick. Does this all seem weird to anyone else? Is it possible he just has a stubborn sinus infection? Poor guy is so tired of being sick and so is Mommy! Any thoughts?