Andrea,
I think some people are simply not sure how "we" prefer to be addressed unless we specifically tell them. As you likely know, there are members here who dress entirely in very female clothing, yet still desire to be seen and addressed as male, it must be confusing to others sometimes.
I suggest that you do not make a big deal out of this, but next time you see her simply tell her that if it is ok with her, you would prefer to be addressed as a female when you are presenting as such. Judging by what you just told us about your relationship, I would expect that she will be fine with using female pronouns for you.
If it turns out that she is not OK with that, well then you can consider what to do next, but I bett that is not going to happen.
Good for you to have such a great relationship with a clothing store manager! I am slightly envious