It's implied that it was done in secret. So it's probably logical to assume that when they cloned Lex the first time they were able to get the DNA at that point. Then when they obtained the Kryptonian samples afterwards they combined the two to create Connor.
Well, this is what I was referring to earlier. At some point (I guess in the Teen Titans according to a poster above), Superboy went from having NO Kryptonian DNA to having Kryptonian DNA. I was wondering if there was some way to reconcile the two versions, but it just seems as if it was a complete retcon of his origin.