A missing endogenous retrovirus in humans, but present in gorillas and chimpanzees?
I think your question boils down to:

Why do modern chimpanzees contain endogenous PtERV1 whereas humans do not?

This is discussed in the original research article:

Kaiser SM, Malik HS, Emerman M. 2007. Restriction of an Extinct Retrovirus by the Human TRIM5α Antiviral Protein. Science 316(5832):1756-1758.

PtERV1 was active after the phylogenetic split of humans and chimpanzees, so any infection would be from separate events. In other words, the endogenous virus was not inherited from a common ancestor:


  Comparison of individual PtERV1 proviruses in gorilla and chimpanzee genomes suggest that this virus was active 3 to 4 million years ago, after the separation of chimpanzee and human lineages.


They hypothesize that modern humans evolved from ancestors that were protected from PtERV1 by TRIM5α:


  Although we cannot rule out the possibility that PtERV1 never infected human ancestors for other reasons, our data do suggest the possibility that TRIM5α was fixed in human populations because of its ability to confer protection against PtERV1 and that modern humans have descended from ancestors who resisted infection.


This does raise the question of why humans were not infected whereas chimpanzees were, despite both containing PtERV1 restricting TRIM5α. This seems to be out of the scope of your question, but they do talk about it in the article if you're interested.