Just because she wears black doesn't automatically make her a magick practioner, especially one of "black magick". She is probably "emo" or "gothic" and a very negative person. Like was said, your picking up on her negativity. Some people project it outward more than others. For all you know the pains you feel could be from drugs, "cutting" or an abusive boyfriend. Or the negativity could just be so strong, your feeling it as pain. I've picked up books in bookstores that "hurt" to touch because someone who picked them up before me was so negative they left behind a strong imprint. When I sense someone that strongly negative, I automatically protect myself. I've been doing it so long, its just second nature now.
Learn to shield and do it everyday before work, and when you are around her, do so in your mind to reinforce the shield. Alternatively you can use an amulet of hematite and black touramine or another amulet of your choice that works for you. It may not eliminate the feeling entirely and I'm sure you'll still notice everytime she walks into the same room. But it should eliminate the physical pain and feelings of illness.