Duplicate folders within themselves on WD My Book

Hi, first things first, I work at a computer repair shop and this question is about a customer's computer.

It is Windows 8.1 and she has a WD My Book 1tb drive that she uses as a backup with Acronis. She brought it in mainly because she wasn't sure of how to use Acronis and for these duplicate folders.
I showed her how to use Acronis and set it up for her and just deleted the duplicates thinking it was from her trying to set up Acronis. Well the duplicates have been reoccurring for her and I can't figure out why.
Making an example might very easier than explaining in a sentence.
Many of the folders are duplicated with themselves, but not all of them. but ALL of the duplicates are inside the original one, not beside it (or however you would word that)
I am speaking to her again today at 3:30 EST and can gather more info
Backup drive D:
Folder 1
-Folder a
-Folder b
-Folder 1
---Folder a
---Folder b
Folder 2
-Folder c
-Folder d
-Folder 2
---Folder c
---Folder d
Folder 3
-Folder e
-Folder f



-Edited because I didn't realize the spacing wouldn't stick in my little diagram.. I hop it makes sense the way it is now.

They are probably from the date or time the backup is done.

I have my son's Mac Book set to have Time Machine to back up on our NAS, whenever he is connected to our network.

It doesn't seem to happen right after the backups though. She has a bi-daily backup setup, but they duplicates don't appear for about a week or so after getting rid of a them all.

Can you provide samples of the actual folder structure and names? That may help ID the cause.

Yeah, I can get that later today and post a couple screen shots of it