when i had problems with nitdroid i did the following steps

But you have to backup your data first>

1.if possible, uninstall nitdroid with the official uninstallation tutorial
2.format your mmc (32 GB) internal memory from pc
3.format your Memory card from pc
4.reflash the n900 fw with maemo Flasher (it may work with the pc suite also (i think both do the same.

i hope this helps you all instead of breaking your heads about thing like those.