Jerry you have rediscovered the reason to make all AR sections longer than the longest train. Many passenger cars have multi-axle pickup where two or more axes on a Truck are electrically connected together even if the power pickup is not being used. As a result the multi-axle truck acts like a Long jumper across each isolating gap In the rails. This causes confusion and even short circuits to the AR controller when a loco or other multi-axle pick up truck also happens to be crossing an isolating gap at the other end of the AR section. I don’t see any way adding diodes will resolve the issue.
Fixes. ... adjust the length of the AR section slightly to avoid simultaneous crossing of the gaps at both ends of the AR section using your particular train car lengths.
Be sure to fill AR section gaps so that steel wheels cannot fall into the gap while touching both rails.
Avoid using wires inside the car to achieve multi-truck pickup to reduce light blinking. (Use some other electrical technique)
If you are not using car lighting use plastic wheels to avoid bridging the gaps.