I recall from a few years back that the Windows defragmenter rearranges files differently than other defragmenters.
That may be what is happening here.
Suggest you check to see if Windows Automatic Defragmenter is scheduled to run or not in the Task Scheduler.
Open Task Scheduler by clicking the Start button , clicking Control Panel, clicking System and Security, clicking Administrative Tools, and then double-clicking Task Scheduler. If you're prompted for an administrator password or confirmation, type the password or provide confirmation.