I know what this must feel like for your partner. Sleeping in each others arms and waking up in the morning lying next to the one you love is gold. And every time I get that rare chance, it is the best moment of my day. I savour every precious second with her, but this is the best part. I am not saying that everyone feels that way, but I know that I do.

I wish I had an answer for you. My gf has many issues that cause similar problems. And while we are long-distance as yet I feel this will become a big issue later on.

Intellectually I know that its her issues that are doing it. But my emotions tell me a different story and its almost impossible to overcome one's emotions. So I keep saying 'its ok' too, while both of us know its not ok.
Your mind tells you its not meant as a rejection, but your subconscious says that it is, and that is so much more powerful.

I think sooner or later you will have to figure out how to face up to and deal with the root of the problem. Whatever traumatic experience it is that is causing these problems. But I can imagine that you are reluctant, because the thought of ever seeing my gf go through that process petrifies me.