When Lyra and Will first meet, the next morning will has corn flakes , which Lyra hasn't seen done before( or at least the process of it) yet, in Bolvanger in the first book, She cues up for corn flakes.
They might just eat corn flakes in COMPLETELY different ways, you said yourself that it might just be the process that Lyra found strange, they come from different worlds after all.
Lyra lived in a college, and as the first book said, she had the servants do everything for her. So, OF COURSE she wouldn't know how to make corn flakes, becasue she had never seen anyone do it before! Same thing at Bolvagar, they probably made them for her.
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