It must be frustrating to know the calcium deposits are there with no answers as to why. Sigh. Are they telling you to watch them? I had what was a minor (comparatively) traumatic birth with my first born. He was way past due by 10 days and I had latent phase labor with no idea that was going on (in that birth was stalled for three days and I just suffered in misery). It's all kind of a blur now. Anyway, he has a developmental delay called sensory integration disorder. It's challenging to be a parent but even more so with kiddos with challenges. Do you have a support group of people in your life?
So, there ARE medical reasons calcium deposits can happen on the brain. From little tumors, to parasites, to future aneurisms. That tests have come back negative is great. But I agree that I would want more answers. How are your doctors in terms of care they give your daughter? She's had a long journey during her young life and I'm sure it is really hard on you as her parent!! Hugs to you.