She could be reacting to the change, it takes a few visits to adjust. If you like this doc then wait it out and see if it gets better. Also ask the doctor tatics that you can do to help your child in being calmer during a doc visit they can usually give you a few things to try for the next time.
I always let my daughter bring one of her favortie toys or stuffed animals to help her feel secure and in control. I usually say maybe the doc can check out the toy/stuffed animal first so we know if it is healthy. The doctor usually checks out the toy first to show what he/she will be doing and sometimes the doctor lets my daughter do the check up on the toy. This helps the child feel in control and in the know. Ask the doc to play along with this, I think most ped would do this.
Does the exam room have toys, if so distract your daughter with those, if they do not have toys bring our own. My daughter ped would ask her about the toys first instead of going right into the physical exam. Just getting your daughter to feel comfortable will help.
You could also go to the library and check out some doc books and read through them so your daughter feels more in the know of what is happening... I went to a book store and bought a few (doc, dentist, hospital collection).