Possibly controversial view, but I think that these differences are largely socioeconomic in nature. The US justice system does not treat poor people kindly, regardless of their skin color or ethnicity. "Justice for all who can afford it" and whatnot.

(Of course there's also the odd case of a racist judge, but my impression is that it's by far the exception.)

Edit: The paper you linked does raise some very interesting questions about the motivations behind various government policies, however.