Interesting. I have to say I've not seen this problem, however, if I understand correctly, cloning is being used to copy the image from a working Rev.C BBB to other Rev.C BBBs? I guess I'm a little confused, as I'm wondering why? If you have a flasher-image on an sdcard, why wouldn't you just use that to flash each Rev.C board?
IN my case and probably others. I have created overlays for a custom cape. Added libraries, software, image etc. I documented it this time, but it took 2 hours to do it. Ok, I was side tracked some, but with cloning you turn it on and wait for the LEDs to stop blinking. Who cares if you get side tracked.