Do you have HIV and Ebola confused? They don't know where Ebola hangs out when it's not in humans. By comparison, it's pretty certain HIV is a mutation of a simian virus that jumped to humans in fairly recent times. The ancestral form is still around in monkeys and apes.
Viruses go back and forth between species. If pigs and chickens and humans have influenza, where did it come from? Did the pigs get it from the chickens? Did the chickens get it from the people? Who knows?
SARS infects people and civet cats. Did the cats get it from the people, or did the people get it from the cats? Who knows?
If a certain percentage of Europeans are immune to HIV - fairly high, actually, 15% of some European ethnic groups are heterozygous immune - that would tend to suggest that at some time in the past, HIV was endemic among Europeans or their ancestors. Contrary, if almost zero Africans are immune to HIV, that would tend to suggest that HIV was never endemic in Africa before.
In Africa, it is widely believed that HIV was introduced along with vaccines. I am not arguing that this is a fact, only that Africans have been living among chimpanzees for hundreds of thousands of years without coming down with HIV. But still, it's a better explanation to "why HIV now?" than most other explanations.
In the meantime - here's an article speculating that the reason Europeans are immune to HIV is plague, not smallpox.
http://www.wired.com/news/print/0,1294,47586,00.html