I have a pretty big issue with my phone.
If I plug the phone to a computer or to a wall recharger I have the green bar on top of the screen saying "not recharging".
I have tryed with different computers, adapters and cables but is always doing the same and now I have 6% left...
I have removed the kernel but didn't make any difference...
If I plug in the phone while OFF the orange LED blink twice and then the green appears for a quick moment and that's it...I can see the NOKIA logo coming on but after that nothing else happened.
if you had let your battery drain completely then that might be the case since N900 does not like charging a completely drained battery. have you tried charging just the battery with some other phone using similar battery or external charger?
if the battery charges then you might want to completely restore your phone including the EMMC and i think i read in some other post that you might be able to retrive your data from the phone before flashing using Ubuntu or something.