The USB charging for N900 does not work very well, search the forums there was an extensive study on how N900 looses battery even though it was plugged in the USB. Ideal charging for N900 is always power outlet.
And also, N900 does not power the battery to charge or do anything once the battery has been completely drained, you will have to use either an external charger or if you or know anyone with Nokia 5800 you can charge your battery through that.
As you said that you saw the green light which I have never heard or experienced if the battery was completely dead.
Try to re-flash including the EMC, always flash the firmware first and then the EMC.