Answer:
Joy had always controlled the core memories, she kept them as happy memories. When sadness first touched one Joy would try deperatly to change them back for "Riley's sake", and did everything in her power to prevent any more from changing. Eventually, Joy had to make the decision of alowing the other emotions to touch them and change them. The stakes there for her were mainly when she had to decide to alow the other emotions to change the core memory's feeling. They were internal because, Joy truely felt that the core memories needed to be happy ones, and nothing but that, and that's one of her biggest struggles (internally that is), Joy wanted to keep Riley happy!