Board Thread:General Discussion/@comment-10941901-20130628153213/@comment-4913740-20130701031455

It's a very confusing subject, we should just accept that it's John, and people like Zero and Boss called him Jack because they were close to him and knew him (because as stated, Jack is a nickname for John so it could be both.)

And he told Ocelot it was John because he respected Ocelot in combat enough to give him his real name.