Sounds like she has what I have... ADD inattentive type. I cannot focus or realize how much time passes. I used to be well behaved and had good grades. It sounds very similar.
The sounds could be a variety of things; tourretes, autism, ADD, or even plain restlessness. (I live with two autistic brothers and one has tourretes. I personally have ADD which I didn't get diagnosed with until my 11th or 12th grade year cause the school was denying something was wrong... all of us are professionally diagnosed by a psychiatrist for adolescents.)

I would take her to see another doctor for a second opinion. After all, it can't hurt just to be sure. If the doctor says she needs medication I would not fight them about it. The medicine does help to an extent but even then getting extra support from counselors and the school are good ways to go as well. I hope you can help her find some peace of mind and get this mystery solved! Good Luck!