Like MJB, I had a skittish kitten. He would hide if I got too close and flinch away if I (or anyone else) tried to pet him. Maybe he had bad experiences with people before or maybe he was just naturally skittish.
For a long time I thought I was going to have a cat who, well, just didn't like me much. As the weeks went by I talked softly to him, tossed treats to him, moved slowly around him, and just tried to make myself seem as non-threatening as possible. Gradually (over several months) he gained confidence and warmed up to me. Now, several years later, he rubs against my ankles, mews to be petted, and several times a day rolls onto his back and meows until I give him a tummy rub.
Your doggy is going through a confusing, frightening time of transition; stop chasing her and SHOW her you are not a threat by letting her come to you. You will have to be patient. Do not take the fear personally. I know it's hard to do your best by an animal and still have it stare at you like you're Godzilla, but patience, gentleness, and love are the only things that can resolve the situation.