It definitely sounds like the cable itself has a bad connector or wire (the red interconnect for the white connector) or one of the pins isn't seated or crimped adequately..
It happens pretty frequently now that these cables have been out for awhile.

 

A friend and I ran into this as well this winter. Though more less the cause has been covered, I think it might also be an issue of ECU temperature. Sounds odd maybe at first, but I checked voltage (I had the same idea without seeing this thread until today) and it was 12.63v so more than adequate. I sarted the car and got it to temp and it was okay.

Lucas initiated a flash and had it stall (a IX MR) halfway through and then he was stuck as was initially posted here by John. He pulled it in the shop and just while it sat inside and warmed up (outside temp was below freezing) while he looked for a battery charger was enough that he went back and reflashed it without any issues.

One other trick I have found that works is link with Evoscan, do a DTC check, or at least start the car (dont have to even warm it up) and log for a few seconds. Turn it off and its enough to flash without issue.

John