I know my response is coming in a few days after everyone else's, but maybe this will help. I had staining on my teeth when I was very little - when my permanent teeth came in. It was from a combination of fluoride, the water source where I grew up, and medication I had to take due to having severe pneumonia. I ended up having bonding to cover the staining (it was my front top teeth, so it was very noticeable). I would not suggest this route, however, because it commits your child to a lifetime of (potentially expensive) cosmetic dentistry - I have now had bonding, veneers, and have had to move to crowns on some teeth. Ugh.
I also have a mouth shape where my upper lip does not naturally meet my lower lip (you wouldn't be able to tell just by looking at me, but it causes my mouth to stay open when I sleep). People with this mouth shape generally have more cavitites or tooth decay because you don't generally salivate as much, and salivation is important to reducing the harmful bacteria (or whatever it is) in your mouth. So there are lots of reasons why your daughter may have staining, and her mouth shape, water source, medications, and just genetics are all possibilities. Just discuss it with your dentist and get second and third opinions, if you feel it's necessary. Lots of people have problems with their teeth for reasons other than lack of care...do not let anyone accuse you of neglecting your daughter's teeth. My parents were meticulous in their care of my teeth, and I still have had many problems (hopefully your daughter won't!). I wish you the best of luck.