One time I relied heavily on the ntfs-3g driver and it killed my ntfs-partition. Since then I always check if any mounted ntfs partition is umounted properly. For automation here is a code snippet for debian (ubuntu?). If a mount point in /media cannot be unmounted there will be no shutdown.
for f in `mount | grep /media/ | awk '{ print $1; }'`;
do
! umount $f && exit
done
shutdown -h 1