Torchwood has been looking for the Doctor since 1897. They didn't find him until 2006, in spite of the Doctor being prominent with U.N.I.T. throughout the 1960s and the 1970s. Why not?
According to the
http://www.torchwood.org.uk/html/jack/snaps.shtml Jack appears to have held prominent positions in Torchwood since 1961. Has Jack been fudging Torchwood's records to protect the Doctor for 45 years? Has he been collecting the Doctor's "flotsam and jetsam" and storing them at his office to keep them away from the London branch? Did he set off the "Bad Wolf virus" mentioned in Love & Monsters that protects the data on Rose? It fits Occam's Razor.
If my theory is correct then it's possible that some agents Jack has trained have gone on to work for the home office in London. They could have instructions to look out for their old boss and redirect Doctor-memorabilia his way when they get the chance.
So far we've only seen two episodes. Knowing my luck, something will come up in the third episode that will completely blow this theory out of the water. But until that happens, it's the most elegant, the most logical, and the most romantic explanation. That's a winning combination in my book.