Has she had a strep test, Mom? Sometimes strep hits the stomach instead of a terrible sore throat and high fever. This has happened to my own kids. One of them had a sore throat (like your child) and I asked my ped for a strep test. She didn't really want to give him one because she said his throat didn't look like a "strep throat" and he didn't even have a fever. But she did it to placate me.
She walked out into the waiting room and apologized to me in front of all the people out there - she said to her shock he DID have strep. So I would take your child back to the doctor and have this checked. If he tested her but the strep wasn't strong enough to show up, I'd have him check again.
I am SO careful with strep because my sister got scarlet fever because her strep was misdiagnosed as a virus. What she went through with scarlet fever was scary. You should ALWAYS get strep treated, which means you need to know if strep is present.
As far as your question of whether up to 100.6 is a fever? Absolutely. Her body is fighting something. Whatever the temp is that higher than a normal temp is a fever.