I was one of those kids who cried when I was taken to my first school. I'll share some of my experience/perspective as a little kid.
My first school was in the school district of my dad's business, sort of on the way there for him every morning. So he would take me there, but it wasn't close to my home, or really close to his work either. I don't know what it was about the place, but it felt so alien to me. And I feared being separated from my mom, as if being so far away, I might lose her or something. I spent months crying and moping, both in the car on the way and at the school. Yet all the while being a "good student." My parents and my teacher were worried and at their wits' end. My fears of feeling abandoned or being unable to reach my mom in case she needed me (yeah - even little kids think like that) really scared and upset me. And I was afraid to forget about her. Perhaps this was in part because I was a first born. And I felt very responsible to the family to be responsible for my mom's sake as well as my little brother.
After a few months, my parents finally addressed my extreme fear of losing my mother and decided to transfer me back to the school in my own neighborhood. Not only did the place not feel alien to me this time, but my fears and crying literally disappeared overnight. In my child's mind and emotional reality, going to school wasn't the issue - it was being asked to be so far away from home and mom. But going to school closer to home was a threshold I felt I could successfully handle. And the people seemed more like home to me there than the people at the other school. Even though I liked the people at the first school, they were nice and I did (after some time of crying) have fun and enjoy some of our activites - they still felt "too far away from home" and too "not safe" to me for my desire to feel certain that my mom wasn't going to disappear out of my life somehow while being so far away. As a child, I was very spatially aware of just how far away I was from home, unlike many kids I guess.
Anyway, when you told your story, I could feel that little girl inside of me again who was so afraid I might lose my mom. Doesn't have to be rational, but it was real. And I couldn't explain all I felt to my parents either. To me at the time, it felt like my parents were asking me to make a sacrifice I just couldn't feel I could face. Later when I was a little older, they were able to transfer me to another school closer to dad's work without any fear or trouble from me or my brother.
So I guess my take is simply see if there's a fear about what you and her daddy mean to her and all. She loves you so much and she may have a fear that to her, being asked to be away from you might somehow betray that love. Just love her, help her feel secure and see. Perhaps some new insight will come to light.
I hope this helps.