What could these symptoms be?

My toddler woke up with a fever of 103.2 yesterday morning and I gave him some children's ibuprofen to knock it down. The only other symptom was he said his tummy hurts. He went back to sleep once his fever went down and was fine for a few hours when he woke up. He even ate breakfast but then his fever started going back up shortly after and he got chills and complained again that his tummy hurt. Hes had no diarrhea or vomiting by the way. So I took him to doctor and described his symptoms and he said he had some throat infection and some chest congestion and prescribed him some tamiflu and amoxillin. When I got him home he slept for several hours. I finally ended up waking him up and he was fine from about 4 30 in the afternoon till bedtime in which his fever showed up again so i gave him some more ibuprofen. He did eat his normal amount at supper time but he did not eat lunch. Today, he was very fussy when he woke up but no fever. He ate breakfast and seemed to be okay up until about 2 30 when his fever showed up yet again so I have given him some more ibuprofen. He's fine when he doesn't have a fever. He's doesn't even act sick. He's not coughing. His nose isn't running. He did complain that his tummy hurts when his fever just came up again. I've been giving him his antibiotics since yesterday evening. Also, my husband brought the flu home from work about a month ago or more in which I then got it and then my toddler got it but it didn't hit him as hard as it hit my husband and I . He just seemed to get a really bad cough that he kept for weeks and just got over about a week ago leaving me to think his chest congestion was gone but the doctor says it's not. I am so confused. I don't know what he has right now. I'm hoping it's not swine flu because for one he's only 3 years old and two I'm 36 weeks pregnant. He does go to something called mother's day out twice a week so he's around other sick kids I'm sure. I am just very worried. Does anyone have a clue what it could be or has your child dealt with the same thing recently?