Because he was actually following a lead on a dirty bomb. He actually thought that the White Portuguese was a person, not a ship, remember?
He even thinks Lex is the WP. That's why he goes to get information from his servers.
Once he decrypts the drive after the Flash Point, only then does he learn that the WP is a ship and that it is importing the K-rock into Gotham.
He was looking for the rock AFTER the Flash Point.
This is confirmed by his surprised look AFTER he sees the WP ship's photos. He never even knew that it was a ship and not a person, why would he know anything about Kryptonite?
He then tells Alfred that the WP is a ship, but doesn't tell him anything else. Alfred picks up that Bruce is not telling him everything. So he tells him that he is not good at lying to him.
Bruce then reveals what he has just learned to Alfred and states his intentions which have come into place thanks to the Knightmare.
And thanks for the appreciation boose!