Your experience sounds quite familiar to me, even though I have only experineced this on ANA. Every time I fly with them in premium classes I get the full gaijin treatment.
Japanese pax around me are pampered whilst I am mainly ignored.
Consequence to me: I don't fly Japanese airlines anymore!
Talking to Japanese friends they thought it probably has something to do with poor English language skills of the crew members. I didn't buy that excuse though, as I have had numerous flights where I got treated badly compared to the Japanese pax.