Are you sure you bought a Japanese SIM? I thought Japan has no GSM service -- only 3G CDMA -- and therefore phones from practically anywhere else will not work in Japan. If you found one, let me know where you got it so I can get one for my next trip.
I was there in June of last year and didn't even bother with my unlocked GSM cell as it would not work. I was only there for five days so it was not worth buying a phone over there.