Thanks Drax!No, files on the SD card have no effect on payload injection. The only variables are your console, the USB cable, and the device sending payloads. If you haven't done so already, try swapping the USB cable and/or rebooting your computer (assuming you're using that to inject payloads).
Hmmm. RCM being detected no problem and having changed out cables with the same result would seem to imply it's not the cable...
Drivers perhaps? If it's the console, that may be a lot harder to figure out I'm guessing.