So, may have found a non-virus origin for this.
I had recently installed the Artemis Spaceship Bridge Simulator game for a LAN party along with its update patch. The two directories that suffered from this problem were the two places it tried to install, first the program files, then the Games directory that I usually install games to.
I think there was a problem with one of the self made installers.
I'm going to uninstall it and try installing again, just to confirm it and assuage my worries.
EDIT: Confirmed. It was the installer that was broken.