Comment 2 for bug 223280

I guess you are referring to "The OS configures the setting in a too late stage during the boot process, only after the NTFS volume was already mounted.", however the volume in question was mounted after booting via Nautilus.

In any case I think rdiff-backup should handle this more gracefully, since it is supposed to store backups even on filesystems that do not support all filenames that the source filesystem supports.