User blog comment:Weedle McHairybug/So, why did Big Boss react with confusion in regards to Cipher? (Spoilers)/@comment-188.81.208.66-20120324171006

I believe Big Boss might have been unfamiliar with the name "Cipher" itself, seeing as the organization I knew referred to itself as The Patriots. It's not contradicting anything from previous games, Big Boss simply didn't know their new codename, but he later connected the dots as he talked to Kazuhira.