fuzzylogician: Thank you. Those are really helpful suggestions, and I will definitely keep them in mind moving forward. I'm sure she doesn't realize it, which is part of why I'm confused about the whole thing. It seems like a strange disconnect. And yes, those differences between letters written for male vs. female applicants are concerning.
ImpulsiveNixie: Yes, I do think that I could be particularly sensitive to her interactions with me because I admire her, although I think that is a gendered framing of the situation as well, but there is a marked difference between being told you are going to be a star in your field (her reaction to my colleague) and being told not to "read too much into" the positive language she is using to describe my work to others in the department. It's not that she is less willing to compliment me, but that those compliments come with a disclaimer, that bothers me. I know that she sees promise in my work. I'm just troubled by the way she responds to it and to me.