The whole story of Jack Harkness is a mess, to tell the truth.
He's a time agent from the 51st century. Okay, then he goes rogue and goes back to 1941 and becomes a volunteer pilot. He hooks up with the Doctor and Rose. The Slitheen bitch shows up in Cardiff and the rift opens up right where Torchwood Cardiff is supposed to be stationed. They don't show up.
He's killed by the Daleks and resurrected by Mega-Rose... travels back to the late 1800s looking for the Doctor, falls into Torchwood, co-exists with his WWII self, but claims he can't find the Doctor even though he knows exactly where and when the Doctor will appear in London in 1941... not to mention the 19 million times the Doctor will interact with UNIT later in the 20th century.
But wait... he goes back to Roman times and gets buried for 2000 years and stored in Torchwood's cryovault... all the while he's there and he never looks in that vault.
Jack Harkness was a good idea for Doctor Who. He started as a good idea for Torchwood, but along the way he became a plaything for RTD's tortured imagination and sporadic writing skills.