Here are my observations:
1) Some units cannot program and they start up in neutral conventional - root cause was the antenna falling off the top of the shell and grounding on the frame
2) Some units cannot program start up in command mode -switch wire to main mother board was not engaged into its connector
3) Some units cannot retain their program when power is shut off and revert back to ID no. 1 : This is a software issue and they must be sent back to Lionel for a reflash
4) Some units making a loud ticking sound: The sensor on the reader board is hitting the flywheel ring. It will eventually ground the ring down and the locomotive will take off or run erratic. - I pulled the flywheel and gently pried the sensors apart to provide spacing for the flywheel ring. My E6's has the same issue.
5) Some units cannot program ID at all - Bad program / run switch
You may see additional failure modes. This is what I have found so far.