We have been going through the same thing in our house!! My son(age 9)had strep the last week in February. Two days after he finished his amoxicillin he spiked a fever and had coughing/congestion. He tested positive again for strep. I was surprised he had strep because usually they don't have other respiratory symptoms with strep. The doctor said my son probably had a virus in addition to the strep. My son was given a higher dose of amoxicillin. We were doing everything right - throwing away toothbrushes, putting his school recorder through the dishwasher, etc., but he came down with strep again two days after the second round of meds. My son did not have a fever or any symptoms of illness except the toxic throat during the third bout of strep. The doctor gave my son Omnicef, which seemed to do the trick. Several days after the meds were gone, my son had a "clean" rapid test and lab culture.
Four weeks later, my son woke up with a fever, headache, and stomach ache. He was miserable, until he took a two hour nap that morning and woke up completely normal, asking for pizza. I took him in the next day to check for strep, but his tests were negative. A week later, my son had several episodes of diarrhea one afternoon. The diarrhea continued off and on again for two weeks. The doctor sent some samples out to the lab, but everything was negative again. My husband came down with the same bug, and was much worse than my son. DH lost 7 pounds in less than a week.
During this time my son, who never had allergies,developed very bad ones, which seemed to progress to a mild cold last week.
I was very concerned and called the pediatrician, thinking my son needed some kind of immune system testing - after all, my son had perfect attendance the last two years. I was told that this was an extremely bad year for illness, and that many parents called with the same worries as mine. The dr. said that children who are almost never sick were in his office multiple times this year, and that there are many bugs, including a bad stomach one still going around. My son's teacher also told me that the winter/spring were very rough in her classroom. My son takes a multivitamin with extra c and a probiotic, but they don't seem to be helping. The doctor said he would order some tests if the pattern continues over the summer. We sure are glad that school is finally out this year. Hope your son feels better soon!