Can you copy the snippet from /etc/init.d/rc.shutdown to a standalone script and debug?
edit: Perhaps the ntfs process is killed by the preceding killalls. But that introduces an interesting catch-22, as the extension processes should be killed before umounting and removing their extensions.
If that's so, then I don't think there's a good solution to this problem, and having the tce dir on ntfs (any fuse really) would just be unsupported.