Oh, dear. I am not surprised that your puppy doesn't want to play with you like before you flipped her over. That technique is called the Alpha Roll is is considered outdated and dangerous and should only be used in the most extreme cases of aggression by professional dog trainers. Since the only time a dog will flip another dog over on it's back is to kill it, having their owner do this to them traumatizes a dog and can make them very fearful.
http://en.wikipedia.org/wiki/Alpha_roll
Try to remember that your puppy is just a baby. She has just left her mother. Now is the time to bond with your puppy and gently help her become a good canine companion. Dogs aren't much different than people. They thrive on praise. Harsh discipline will make her fearful which is probably why she is afraid to come out of her expen and growls at you.
Have you spoken to your breeder about the problems you are having? A good breeder is the best resource you have.