Here's something that I just posted in the New Positivity thread in the BvS subforum, which I feel could be added here too since it ties in with what actually happened with regard to Bruce and his knowledge of Krytonite before the Knightmare.
I'm actually feeling really confused about this thing now. Bruce tells Alfred that, "It's a weapon, a rock, capable of weakening Kryptonian cells.
The first one that was big enough to mean anything turned up in the Indian Ocean, three months ago."
And if we recall the flow of events, the first scene after the MoS battle is the discovery of Kryptonite in the ocean. Then later, after that scene, we see Batman interrogating that goon who he brands but at that point he is asking him WHO, and not WHAT the WP is. We know this because the goon answers, "I don't know who he is, I don't know who he is."
So going by this flow of events, I now feel it would be safe to assume that Bruce DID know about the Kryptonite and what it can do since he could have possibly gained that information from USAMRIID, but most probably didn't know that LexCorp was involved since the research happened at the AMRIID facility instead of LexCorp, which was just taking a copy of that research for themselves.
This means that Bruce WAS in fact lying to Alfred about the 'dirty bomb' for some time.
Bruce would probably have come across mentions of the White Portuguese during his investigation into Kryptonite and it's location, and it would have lead him to assume that the WP was a buyer of the K-rock.
He didn't actually know it was a ship till he gets Lex's files. And he didn't know that Lex was involved until he cracks Anatoly's phone and gets that info.
So the flow of events goes like this >
1. Kryptonite found in Metropolis rubble by Lex's 'Rebuild Metropolis' crews.
2. Lex performs research via proxy at USAMRIID and gets the results.
3. Batman gets wind of this research and gets to know about Kryptonite and what it can do.
4. Bruce starts investigating the world for more mentions of Kryptonite.
5. Lex has his people searching the World Engine crash site for more Kryptonite.
6. The larger sample of Kryptonite is found in the Indian Ocean.
7. Lex begins the plan to smuggle it into Gotham after he is denied the import license by Finch.
8. The White Portuguese code word is put into effect by Lex who knows it is a ship but other than him and his people, no one knows.
9. Bruce catches wind of the White Portuguese and he thinks that is a buyer of the Kryptonite and so he starts tracking any mentions of the WP.
10. That leads him to the human trafficking goon who leads him to Anatoly.
11. He tracks Anatoly and clones his phone after the boxing match.
12. He finds that Lex is involved and could possibly be the WP.
13. He hacks into Lex's servers and gets the data he was looking for all this time.
14. He begins the decryption.
15. Knightmare happens, he learns that Kryptonite is essential or else he WILL fail (he remembers his death in the Knightmare).
16. He learns that Superman is a confirmed threat and that if there is even a 1% chance from his vision that Superman is a threat, he must take it as a certainty.
17. He wakes up from the Knightmare and goes through Lex's files and learns that the WP is actually a ship and not a person and that Lex was going to import it via sea.
18. He tells Alfred about the ship but doesn't mention the Kryptonite.
19. Alfred who has picked up on the fact that Bruce was lying about the dirty bomb for some time, confronts him with it.
20. Bruce reveals everything to Alfred and then goes to attack the convoy at the port.
Confusion eliminated!
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