I just made a fresh install of windows and installed CIS 8.
I observed strange behavior of the auto-sanbox feature installing software and windows system files in the VTRoot without my knowledge.
Those applications were nowhere to be found, it was like they were never installed in windows, no shortcut, not in program groups and no entry in the add/remove programs.
I finally found those applications in the VTRoot folder on the C drive.
I can tell you that I reinstalled windows a couple of time before I found it was the auto-sandbox feature of CIS.
I found the problem when I installed Handbrake open source video transcoder 0.10.0 and CDBurnerXP 4.5.
CDBurnerXP was flag as trojan on installed and handbrake was sandboxed and put in the VTRoot directly with no message(no flag as trojan, he was not installed in program files folder and not found in the add/remove program list.
I decided to disable the auto-sandbox feature and reinstalled those two software without any problems.
For the system files, I made a capture of where the files are in VTRoot. Maybe they are not windows system files, but they are identified as system files in the folder.
When a sandboxed application accesses a non sandboxed file that file will be sandboxed so the application can access it. Im thinking this is why you are seeing windows files in the VTRoot folder.