Board Thread:General Discussion/@comment-25709549-20141130223109/@comment-25366375-20141201041902

Kohaku332 wrote: ...But even The Boss called him Jack....okay....I was just confused beause I never in all the games of MG I played herd ANYONE call him John, other than himself at the end of MGS3 People named John get called Jack as a nickname. People called Jack (e.g. Raiden) don't get called John because their name is Jack.

Either way, Big Boss calling himself John should have been your indicator.