Anyone have any experience with this?

We tried using one of those agents who do it for you and the visa was denied... We want to spend two nights in Japan on our way to Hawaii, have plane tickets, hotel reservations and US green card...

if you have chinese passport and USA Greencard, do you not have a USA passport? that'd be far easier. but on what grounds was your visa appl;ication denied. maybe you completed the form incorrectly or something simple?

The Japan consulate does not give a reason for denying a visa and does not allow reapplication for 6 months. I am sure that the agent just scrwed up the application though...

A US greencard is a residence permit to live in the US. It is not citizenship, so a US greencard holder by definition would have a non-US passport.

I just called the Japan Airport Immigration Authority in Tokyo and said that you can get a landing visa for 72 hours with an onward plane ticket and hotel reservation. Myhusband (the Chinese passport holder) will be with myself and our daughter (US citizens), and the immigration officer in Japan said that it was almost certain that a landing visa would be given. Has any Chinese passport holder gotten a visa at the Tokyo airport before?

yes true about the greencard is US residency, but then after a qualifying period one can apply for US citizenship. anyway sounds like the landing visa is an ok option. you can show you're a low risk -child, husband, hotel, outbound ticket etc.
i'd simply go and apply in tokyo.

If the Japan consulate are providing your visa then you should know the problem and reapply your Visa form.