>>16788314 (OP)
Some sort of parasite.
As yet unidentified, it may involve more than one organism, one of which is normally harmless.
Nature abounds with parasites which "hijack" the behavior of the host and makes it do abnormal things. To name just a few that affect humans:
Influenza ( Yes, really, it increases social behavior, makes people want to go out and socialize with others )
Rabies ( causes hydrophobia in humans )
Toxoplasma gondii ( linked to schizophrenia and other mental disorders )
Sleeping sickness.( sleep disturbance and other mental disorders )
There are others, Caused by very different organisms.
Some parasites alter sexual behavior in their host as a means to facilitate their own sexual reproduction. One example includes the bizarre case of Massospora cicadina, which is a fungus that infects Cicadas. Infected male cicadas begin to imitate female sexual behavior. Basically the parasite turns them into transsexuals. Uninfected males mistakenly mate with them and become infected in turn.
>We would have identified the parasite by now!
Not necessarily. Biology and diagnostic medicine is not a closed book. Furthermore we are discovering new species and types of diseases all the time. In fact an entirely new class of microbe with virus-like features, "Sukunaarchaeum", was reported just this year.
Furthermore the parasite which causes homosexuality may have a complex interaction which may make its identification difficult even with modern technology. It may use an intermediate host, it may be in a symbiotic relationship with a benign organism commonly found in humans and thus "hidden", its actions on the human brain may be limited to affecting some individuals only under certain specific conditions. Different forms of homosexuality may be casued by different parasites. Etc.
Then we also have the current inhibition against looking for a parasitic agent. Try securing funding for any research into this area and you will immediately encounter a brick wall.