Truthfully, the fact that multiple engines have exhibited the same issue, I'm leaning more to a wiring issue than a bad board. Both are obviously still possible, but more than one fairly new locomotive doing something odd like that seems to indicate it's something else.
According to the User's Manual for the 6-28344, the reset is just reprogramming the locomotive ID, although it couldn't hurt to try the ALT code that Bob suggests, #2 is the code for many similar vintage Legacy diesel locomotives.
