I'm with you.

It's strange that a newly formatted drive, would show such fragmentation, after being reloaded with files in the manner described.

I can only offer that maybe your software was not waiting for the each file to finish copying before starting the next. Those kind of overlapping copies could produce that result.

It would also thrash your cpu. Kind of like a denial of service attack.

If overlapping copies are taking place, Process Monitor will show it.