On my W10Pro system, if I choose to let the program run scheduled under the SYSTEM account, the user part of the registry backup ends up (almost) empty.
Only when run under the current user account results are as expected.
Before I upgraded the OS from W8.1Pro all was OK. Upgraded the tool from 2.x to 3.1.0 but that didn't help.
Currently running the task as the current user to work around the issue, although that requires login.
As an aside: configuring a task for Windows Server 2003, Windows XP, Windows 2000 is not supported under Windows 10, it seems, if that task is to run under the SYSTEM account. I found that out by editing the task in Task Scheduler and upon selecting the SYSTEM account, getting the message "Running a task under a group user account is supported only on Windows Vista or later. To run a task under a group account, you must upgrade this task to a Windows Vista task."