Since you are running out of options, why not give rsync a try?
Rsync is associated with Samba (see: http://rsync.samba.org/
) and was originally developed for copying across networks. It works fine on local files and only copies files that have changed. Using ntfs files as a source may cause problems, but it's worth a try.
Using rsync is a lot like using cp:
rsync -r /mnt/source/ /mnt/destination/
That would recursively copy whatever was in /mnt/source to /mnt/destination. In a linux-type filesystem setting, you would usually run it like this:
rsync -a /mnt/source/ /mnt/destination/
where -a is archival and is similar to cp archival copies. Since the concept of preserving the owner, group, permission, etc. does not really apply to ntfs files, the -a option might have unexpected consequences when copying ntfs files.
You could always try -a v.s -r on a small directory and see what happens. In any case, you can always run chown, chgrp and chmod after you're finished.
For more details, see: