There is no way to truly know another's mind and all their motivations for their thoughts, words and actions. It may be possible to get a better idea of what's going on if they are the type of person who is very direct and forthright. In other words, no game playing, manipulating, etc. Even then, you can never know for sure because people do lie for various reasons... sometimes for positive reasons as in to just "spare the other persons feelings." Another type of lie is a white lie... a lie of omission wherein they know the truth but neglect to inform others for personal reasons. With that said, please read on...
You do not clearly indicate if you feel that your partner has been one to manipulate and play games or if you feel that she is the type to be more direct, honest and forthright. For the sake of this discussion, I assume she is probably the latter, and then it would be reasonable to suspect that her life before you may have included forms of psychological, emotional or even physical abuse which would then cause her to develop a low self-esteem... a feeling of low self-worth and of not deserving the good things in life.
Perhaps you've heard the old saying, "what goes around, comes around?" As humans, we have a tendency to project our beliefs and expectations outward onto our world and the people in it. So if she was "programmed" through abuse to believe that she has no worth and that she doesn't deserve the good things in life (including you), then that is what she will project outward to you through her thoughts, words and deeds. Her confused sense of low self-worth and undeservability is projected outwards towards you... then it creates confusion in you which you then may choose to reflect back to her in a way that causes you to reject her... hence her projection of not deserving is validated... and then you both get to suffer the consequences. While I can't tell you what to do, if it was me, I would try to understand all of this complicated stuff as best I can and give her some time and support to work through this. Compassion and patience are the operative words here.
From the last part of your question, you state that she still indicates a desire to be with you... but you're confused as to the real meaning behind her words. The big thing to remember here is that it's not really about you, per se... it's about her probable abusive prior conditioning... which would form her currently held beliefs and expectations. From your statements, she appears to be experiencing a lot of emotional pain and confusion... so her statements and behaviors towards you are also confusing and somewhat contradictory. She doesn't want you to leave... but she feels undeserving but loves you enough to not want you to suffer along with her. If she is an honest and direct type of person, she can find a release from her low self-esteem and that in turn will give her more clarity about what she really wants from/with you. And that, in itself, will give you the answers you desire. If she is open to this, find a therapist who uses EFT (Emotional Freedom Technique) or BSFF (Be Set Free Fast) as those types of alternative therapies may turn things around very quickly with a minimum of time and expense required. You can find those who practice these techniques on the internet. It may be helpful to know that these techniques can even be successful over the phone so your location may not be a major concern.
Best of luck to both of you.