Didn't her school record get changed around about the time they ordered her uniform? The admin person assumed she was male and thought it was an error, so changed her gender in the system? I don't think she discovered that/got that fixed when she inquired about her mistaken uniform? From what I remember.
Oh, I see! You're looking for evidence for the theory/possibility that he knows already, not just idly questioning. I suppose it's possible, but I don't think he even knew about her before she showed up in her male uniform (so, after the admin error), and he didn't seem to recognise/remember her from whenever it was that she fell in love with him?
I think there could be things we just haven't been shown, so it's not a possibility I'm ruling out yet.
haha yeah you caught me, it's a theory of mine XD I don't suppose he knew this fact when they first ran across each other at school ( since he does call her with masculine pronouns and all) but after she sparked his interest after the incident, he asks for a copy of her file from the storeroom. It's on chapter 4 I think? We don't get to see him look at it and his behavior in the succeeding chapters in pretty suspicious ...

hmm, I'm suspicious... does the blond dude already know she's a girl? He did check her school records though