At this late point, intermittent wheel contact might just be it. I would put a straightedge over the two gaps, backlit, and see what you see at eye level with the rails' bearing surfaces. Both sides of the tracks in case the one side doesn't allow light, but the other does show an uneven surface.
Well, the problem seems to be resolved.......for now. The problem with fixing something without fully understand why it got fixed is if it happens again, you can't be sure what you did before was really what fixed the problem. I was able to run the RS-1 all the way from one loop to the other, entering and exiting the loops multiple times. It appears that using the west end loop exit to flip polarity for the east end entrance took care of the problem. I even ran the RS-1 through the west end entrance which would flip the polarity opposite of what it needed to be for an east end entrance and the autoreverser was able to handle an east end entrance. Knock wood.
I might have discovered the reason my system wouldn't restart right away after shorting out. If I powered off my wireless throttles before restarting the main system, it would restart without delay. Again, not sure why this fixed the problem or if it fixed the problem. It might just be coincidental. But at least it worked this time.
This was three days of time lost on getting the layout up and running again. While working out these problems, I removed all the locos from the layout to make sure I was isolating the problem. Now I can start putting them back on a few at a time to make sure I'm not having an overload problem. Hopefully I'll have everything running in a few days.
That is good news John. Glad to hear you got things running right again.
Mike