Having lived in Japan myself I can attest to similar incidents. Another point to make is that some people mistake Japanese politeness to mean they are also being "nice" or favourable; Japanese people on the whole are invariably polite, even when they are being rude or exclusionary.

And one last point to make is that in Japan racism has a somewhat fluid hierarchy; certain races are viewed more favourably than others (occasionally markedly so), the amount of racism is also affected by the social status of the foreigner.