Hm, this is a tough one, mostly I have no idea
You can find the canon explanation
here but Smallville doesn't necessarily have to stick too close to that plot, and I'm guessing they won't. Here's an interesting part:
Quote:
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Superman's world was turned upside down as a rocket again fell from the sky to the Kent farmstead in Kansas (SUP #166). This peculiar craft delivered a single green isobar. This isobar, attached to a specialized device Professor Hamilton designed would be able to translate the communication directly into Superman's mind. Upon doing so he encountered Jor-El. This time Jor-El had different news to share with him. He shared that he had intentionally mislead his son to believe that Krypton was a cold emotionless world to help him embrace his adopted home. He explained that he waited to reveal the truth that Krypton was actually a loving place, similar to Earth.
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