Are you doing it on XTLs installed in vehicles? I ran into this problem before, and this is what I did, and it worked; I don't know which one did the trick, but this is how I was able to do it:
1 - I started turning the vehicles on, ensuring the voltage was good
2 - Restarted my computer, unplugged the cable, plugged it back in, reopened CPS, and went right to cloning
It was a pain for the handful it was happening to, but we managed.