We know that in the 51st century, where Jack grew up, everyone is omni-sexual. We know this because Jack has said so (or at least implied so), and the Doctor has said so. I’ve occasionally had theories that the Boeshane Peninsula, where Jack grew up, was not quite as opened-minded as most of the 51st century world. Why do we always assume people in the same time period have the same values? Does everyone on earth in the 21st century think the same? I’d say not. I picture Boeshane as being more open-minded than many parts of our world--it wouldn't be illegal, just looked down upon--but close-minded when compared to the rest of the 51st century universe. Jack would have become more open-minded when he became the first person from Boeshane to join the Time Agency.
But I'm not sure that would actual explain why Jack talks more about his past relationships with men has past relationships with women. For that, I have an entirely different theory. For this theory, I’m going to assume that the Boeshane Peninsula *was* just as open-minded as the rest of the 51st century, and Jack grew up with no concept (or maybe a very vague concept from history books and stories of other cultures) of discrimination on the basis of sexual orientation.
So, Jack is a person from the 51st century who has no real concept of discrimination on the basis of sexual orientation. He becomes a time agent, and finds out about all sorts of discrimination first-hand that he had never experienced in his life. He learned the culture and values of the areas he traveled in, so that he could behave accordingly. But he didn’t buy into those beliefs. As a time traveler from what he considered to be a more enlightened time period, he probably looked down his nose at the local beliefs, and laughed at them behind their backs with his buddies.
And then he got stuck on earth, in the mid 19th century, with no one from his own time to keep him company. The prejudices that he used to see as other people's problems become a part of his daily life. Survival wasn’t much of an issue—dying was painful, but temporary—but he couldn’t ignore the local customs. Everyone he met had been indoctrinated into them. Anyone he might take it upon himself to love or hate (or who might take it up themselves to love and hate him), anyone he might want to befriend, to work with, to date, to sleep with, had to some degree bought into the idea that sexual attraction to your own gender is wrong, is less-than, is bad. If everyone around you holds a certain belief, it can be very hard to hold onto different beliefs, no matter how right you might think your own beliefs to be.
What could Jack do about it? Well, he could simply buy into it. Internalize their belief system, or at least pretend to. Another option is to not buy into it. Stay true to the beliefs of a lost time. Be blatant about it: You think their beliefs are crap. Make sure everyone knows that you don’t have a problem with sleeping with people of your gender.
Jack is obviously aware of the prejudices of the centuries he lives in. In both Out of Time and Captain Jack Harkness, we’ve seen him turn *off* when interacting with men from past decades. He concealed his attraction to them from them, until (in one of those case) the other man made it very clear he was also interested. In the present, however, and in at least one flashback from the past, he is very loud and obvious about his attraction to men. But not his attraction to women. Why not? Because it’s not as controversial. It’s not as big a deal. Jack wants to believe, and wants everyone else to believe, that he hasn’t been affected by 21st century prejudices. And yet, the very fact that he emphasizes his past male relationships over past female relationships shows that he has been affected. Jack is telling himself and everyone else that although he has lived through decades of homophobia, it hasn’t fazed him. Although it obviously has, or he wouldn’t feel then need to make sure everyone knows that it hasn’t.
But pretending probably helps. Like, pretending you are smart gets you better scores on quizzes, pretending you are happy makes you happier, pretending that you aren’t affected by the prejudices around you helps to keep you from completely buying into them.
I haven't seen Miracle Day since it aired, so I won't talk about how Jack relationship with Angelo (who is definitely uncomfortable with his own homosexuality) fits into this, but is surely relevant. I'll save that for another time.