Hi john.
This reply isn't based upon any technical knowledge, just some research after reading about your problem.
From what I've gleaned via google, this seems to be an NTFS issue more than anything else.
Some links here about other folk experiencing the same issue ...
Copying Many Files En Masse from NTFS to NTFS, Fragmentation:
Empty drive - fragmentation problem:
Why does copying files to a new hard drive not defragment it?:
What I found was that files are more likely to fragment. Even files copy to a completely empty drive will fragment ... I really don't get why it chooses to fragment the files.
Taken from here:
Was there any difference between the way you successfully copied to empty drives previously, maybe the software you used, different Operating System?
And on a completely different tack, are you copying the entire contents of those drives to use as backups?
If so, to avoid this increased fragmentation issue, have you thought of backing up the contents of those drives as a Disk Image. A perfect copy of the source drive minus empty space, which can be restored, or mounted as a drive to access the contents.
I won't go into any more detail with that in case I'm way off beam with the suggestion, but there's a lot of info on this forum on Disk Images, and a lot of us use this form of backup for our System Drives and/or data drives. I'll expand on that if it's of interest to you.
You'll probably get some better technical input from some of the other guys, but I've maybe given you something to think about.
EDIT: After raising the Image file option, I was wondering as to whether a Disk Image would be possible on such large drives, but it appears that the size of NTFS volumes/files is only restricted by the size of the available space, and I can't find any size restriction rules in my imaging software, "Macrium Reflect".