VO has never altered any of my non-VO program settings.

I don't know what permission stuff you're talking about; probably a Windows thing. In Linux, VO gets installed into the home directory, so it doesn't need any special permissions at all.

Many of us have been playing for years and years and never had this problem. Therefore, this is most likely, if not entirely certain, an unrelated incident and you should look elsewhere for the cause.

and with the level of manipulation of the game going on I seriously question it's security.

If you are uncomfortable with how VO runs on your machine, I might suggest not using a computer.

On Windows, VO runs in Administrator mode because of legacy reasons.
Maybe VO was somehow infected with a computer virus on your computer. Did you try any anti-virus or anti-malware detection programs?

If you are using Windows 8, you can use the version of VO from the Windows Store, which does not run with administrator privileges.