This is not a contradiction, and it does not render the data out of date. It confirms the closer evolutionary relationship of humans and chimps than either humans or chimps to gorilla.
Once again you show that you have no idea what the data shows. Once again this is not new, I have been telling you that ERV and genomic data shows this for over a year now GGG.
As the data you source concludes......
http://www.plosgenetics.org/article/info:doi%2F10.1371%2Fjournal.pgen.0030007
“Furthermore, we have applied this methodology to four long autosomal human–chimp–gorilla–orangutan alignments and estimated a very recent speciation time of human and chimp (around 4 million years)”
Apparently you can’t even read phylogenetic trees. State CG allows for humans and chimps to have diverged from apes and NOT from each other. That means, even your co-religionists over at the Temple of Darwin are admitting that their human-chimp catechism may be wrong. LOL