Hi James,
I had the exact same issue for a long long time, went thru everything on the car trying to find that hiccup - pop - set code problem. I found the problem would happen with only the ribbon cable attached even w/o the hardware module on the other end so I knew that was the problem.
Tried super clean connection, spacing of cable connector, went to as short of a cable from Kent as possible. I'd never dealt with EMI before and wrapped the cable with foil hoping it would help...nope. I got the flexi shielding from Conleys and installed, still had the problem. Thought maybe my sig lighter power inverter might be doing it so I moved it as far away as possible, no help.
So I emailed kent and we went thru several things then he told me the shielding had to be grounded to dissapate the emi, cool, now I got it so I twisted a bunch of fibers at the ecm end of the ribbon cable and stuck them in a butt connector and ran a wire from there to the ecm, still had the problem, I told Kent and he said the amount of cable in the butt connector isn't enough and that I should make sure as much of the shielding as possible is touching the outside of the ecm so it will ground the EMI as good as possible thru the ecm case and into its ground connection
So far that has totally fixed my problem. I have the shielding running flat up against the back(non chip) side of the ecm and have two places where zip ties run totally around the ecm to help hold the shielding against it. I don't really want to use tape because of the heat of the ecm which will probly make it all sticky in a short time but that would make the ecm slide into the kick panel easier.
One other thing, I'd removed the chip panel for easier access and have now replaced it to make sure no EMI could get into the ecm that way.
Hope that helps, feel free to email me with anything else and I'll try to help.