I tried to download Windows Repair from the Tweaking.com site from the link you posted. IE9 Smart Screen filter blocked the download as malware. Something to check out perhaps …
Anyway, I reset permissions the old fashioned way using the MS SubInACL tool. I don’t want to post the link or details here since I don’t want uninitiated to totally hose their PCs by running the tool wrong. The instructions a MS SE gave are wrong anyway. No surprise there : If your interested Essexboy let me know and I will PM you the details.
I turned off NAV2012 autoprotect since it was interfereing with many of the registry key resets. Then it dawned on me that also NAV 2012 protected keys were reset. So now I am debating whether to reinstall NAV 2012. :-\
A little scary background on why I wanted to reset all my permissions to default. A month or so ago, I was using Process Explorer and decided to check out my WIN 7 service permissions. What a shock! All kinds on unknown user permissions assigned - WTF! So I manually reset all the service permissions but never felt that I had reset everything; hence the desire to do a full registry and file reset. I did research this and since I am running a dual boot, I did come across a few postings that stated there can be crosss-OS migration of permissions when running multiple OSes. But the permissions I saw went far beyond that. I do know that after I performed the manual service permission reset, my incidence of malware intrusion attempts dropped to nill. Also after doing my recent full permission reset, my Win 7 installation is running and booting like when I originally installed it. I am now a firm believer that after a serious malware incident, examining and resetting permissions if required is a must.
I need to add that I double checked my NAV logs and even with autoprotect disabled, NAV blocked SubInACL tool from modifying NAV registry keys. Later versions of NIS and NAV are pretty bulletproof when it comes to anything tampering with it’s internals.