Jim,
This is an issue with some consists and has been since the early days. It's nothing you are doing. The solutions vary and seem to work in most circumstances. One of them that's the easiest to implement is moving the junction lever from the very center of the spline point to the outer edge of the circle. Another solution that seems to work is adjusting the length of the junction, meaning make the frog a bit tighter so the junction is shorter. Will it work for you? Give these a try and see if these help. There are other solutions, but I can't remember them.
My thought on this is it's not caused by other AI drivers flipping levers because the junction is locked due to the close proximity of the train car over the switch, although I have seen AI test flip levers as they try the path for access, and did wonder if this can cause the problem. The issue then could be a timeout thing. The junction returns back to it's original position after a train passes. This is well and good, but could it be that this return-to-home-position is governed by a set amount of time rather than the length of the consist crossing over the junction? If that's the case, then this is where the problem lies. A short consist may work fine all the time because it fits within the set time period. A long consist, especially one with really long freight cars or lots of long passenger cars, will take longer to pass through the junction, and this is where the problem is. Since this consist is taking longer to cross through, the junction is flipped anyway based on the internal timeout code, and that catches the consist and derails it.
