I had problems with this to.. It's becouse the mounts is defferent on nitdroid then it normally is on a android phone, and therefore it's having trouble remounting /system with rw permissions. You could try remounting yourself though terminal emulator or adb shell (if that working?) then it'll probably work.

Edit: I'm not using my n900 that much anymore becouse I "upgraded" to a real android device, and it's also kind of late, otherwise I would break out my n900 and give you more detailed instructions. But, I guess you'll figure it out. If adb is working, you could try a adb remount, that remounts all partitions with rw permissions on my rooted android-device atleast.