The first 気のせい refers to the girl's eyes, the second これも気のせい clearly refers to the engraved note. However, while the first time round there was actual doubt, the second time it's not so much the case: the note is clearly there and he knows it, but he chooses to ignore it and makes an excuse to himself for doing so: "Oh, I guess this was a mislook as well". The だろう enforces this: he knowingly goes ahead with the false assumption that the note isn't really there, without looking at it further to verify. He closes his eyes and acts as though it doesn't exist.