Ok by default on windows 7+8, FARR (and all of my apps) will store their config files in the user Documents folders (should be My Documents\DonationCoder\FindAndRunRobot\and so on).
It no longer legal for programs to store their files in the Program Files directory.
However, with FARR you can customize where you want the files to be stored by editing the ConfigDir.ini file inside the FARR program files directory. Just remember you need to point it someplace that FARR has permission to write.
Let me know if that helps.