If the events of Torchwood and Doctor Who are considered together, there are four different versions of Captain Jack Harkness in the World War II time period. Here they are in chronological order of his own timeline…
JACK #1 is his appearance in Doctor Who ‘The Empty Child’/‘The Doctor Dances’; his significant first encounter with the Ninth Doctor and Rose Tyler. The night that changed his life!
JACK #2 appeared via Vortex Manipulator in 1869 London (part-seen in Torchwood ‘Fragments’), following the events of ‘The Parting of the Ways’. The device short-circuited and the teleportation was left unusable, which meant he lived through World War II once again, part of which we glimpsed in flashbacks featured in Torchwood: Children of Earth.
JACK #3 is the Jack seen in the Torchwood episode ‘Captain Jack Harkness’ in Series 1 in which he is sent back in time to this period with Toshiko.
JACK #4, however, is significantly less mobile as this time round he was buried alive in 27 AD (Torchwood ‘Exit Wounds’), only to be dug up in 1901 by Torchwood and put in a cryo-chamber with instructions to be defrosted/woken in 2009. Therefore, this fourth WW2 Jack was frozen throughout the time period that all the others were wandering around.