I'm sorry, it's just... yeah, this is kind of what I do, so I don't really have an off mode with it.
That's... peculiar. I mean, for her, not for you. You were right in holding back from sex when she was emotional. I don't know anyone in their right mind who would have sex with someone while they were crying, that's just um... weird.
My best suggestion would be to talk to her about it in earnest, without letting the conversation derail. The only way either of you will know what's going on is if you talk about it together.