I can't imagine how that's possible... It takes a minute or two to wipe settings, so it would be pretty noticeable. If it happens again, please save the settings from the controller and send them to me so I can see if there's anything unusual going on.
Are you saying that this happened without the editor connected? Sending the wrong settings from the editor would definitely cause the problem, it's harder to see how it would happen without the editor (or flash drive) involved.