Maybe she is slowly coming up to the logical conclusion that CW does these helpful and thoughtful things to her because, despite their history, he has a "warm and amiable heart".

I agree that she has no time to analyze things over during the Little Walter incident--she is overcome with strong sensations. But during the Winthrop walk, perhaps, then she could more rationally see and add up that these gentlemanly--even friendly--things he does for her is due to his superior character and because of unacknowledged friendship.

In fact she totals all these incidents at the end of Chapter 12 (after further events such as his praise of her and her capabilities) when Anne interprets, even concludes, that his asking for her advice is an actual "proof of friendship".