Hi CaptainKirk. I'm sorry that you're going through this. Without offering this as an excuse for your girlfriend, most people do not understand what it means to be trans, or to question one's gender or sexual identity. My wife, a trans person, has this same issue all the time with people who have known her all her life. Her parents still sometimes refer to her by her 'old' name and by the male pronouns. I have friends who congratulate me on being 'brave' enough to be with someone who they see as being a girl who used to be a guy. They do not see her as what she is: a woman. I'm not sure what to tell your girlfriend, except that, if you have told her in the past how you feel about it, I would just be blunt about it and say something along the lines of, Look, I care about you, but I feel you are disrespecting who I am. This (outline how you prefer to be acknowledged) is who I am and I need you to stop referring to parts of me I don't wish to recognize. (Or however you want to put it, whatever works for you...)
Most people still view being transgender, transsexual, genderqueer, gender variant, etc, as something 'subversive', and don't take into account that someone who is trans is actually that gender, and not just playing dress-up or make-believe. I try to educate people whenever I can in the hopes that one day trans* people can enjoy the same rights and freedoms as anyone else, including being identified as they themselves identify. Everyone should have that right. Good luck.