SandraHi Natalie,
Could she be allergic to the antibiotics? Sometimes it takes a few days to react. I found out I was allergic to bactrim when I took it for strep throat and woke up with a puffy face, aches in my legs and very tired. They switched me to zithromax and I did great!
As far as the fever, a virus can last a week or more in some cases. My seven year old son spikes fevers quick. He goes from normal to 103 in 6 seconds flat! His last viral infection he had a fever for a few days then it seemed to go away, then a few days later it came back and hung on. My 4 yr. old also just had the same thing happen. Both are non CAH.
I would check the meds first then wait a few more days. It sounds like her body is trying to fight off an bug of some sort still with those slightly elevated temps.
Good luck, I know how frustrating it can be for all!
Sandra