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She just meant that he was acting differently, though she probably couldn't figure out why she felt that way, because she couldn't explain it to Sora very well.
Kairi was a Princess of Heart, Riku was becoming obsessed with power. Sora had two hearts, his own, and Vens. Vens was nothing but light, as Vanitas, his dark part, was taken out. No wonder Kairi felt more comfortable talking to Sora, the one who was chosen to wield the Keyblade regardless of Riku being the intended wielder.