Douglas,
Great explanation. Reverse connections are common, especially for timers buried deep in a fuselage. Also, trying to program on the 2nd ESC lead is common because you can't visualize the connectors if the timer is buried. I always recommend putting an extension on the programming pins and leaving it in place. Also leave a lead connected to the Jeti Box. Programming the timer is then simple by connecting the leads/extensions and are always in the correct place.
In Frank's case above, everything seems to works except programming. We walked through all connections everything seemed to work when connected correctly, but its would not program and said waiting for device. That seems most consistent with previously powering up with the pin shift as described.
I hope that you knew that from your knowledge base and didn't have to learn by experience and lots of timers :-)
Thanks for the information,
Fred