I tried it on three computers all using Windows 8.1 Pro 64-bit with the exact same results, which do not get repaired after restoring the backup.
The new version seems to be getting into areas that it should not be, but the entries being cleaned out appear to be benign and non system.
It's temp files, lost registry keys, and a couple things that look like routing stuff you would want to clean out.
For whatever reason the user desktop and the systemprofile are being intruded into very heavily.
I tried some filters to prevent this, but so far I am having to do a full restore to fix my problem.