At that age, you're doing the right thing by brushing her teeth twice per day! Do you have O. of those fingertip brushes? I always liked those when my son was younger.
If I were you, I would take her to a pediatric dentist who can answer ALL of your questions. Just so you have peace of mind. If the teeth are discolored (brownish/grayish) it could be from a trauma (smacking her teeth during a fall, etc.), resulting in a damaged nerve or root of the tooth. This happens to lots of kids. My son had O. front tooth that was slightly discolored from a trauma. No amount of brushing will "turn" that tooth back to white.
When my son developed a small abscess on the gum above his front tooth, our dentist told us it was an infection from the nerve being damaged by that previous falling episode (years earlier) and it needed to be extracted, otherwise, it could adversely affect the permanent tooth beneath it.
I would say you need to find a reputable dentist that caters to kids and have her examined. As long as there is no infection I wouldn't think her permanent teeth will be damaged. Good luck!