I’ve not done any isometric kind of stuff, but if I had to guess I’d say the camera is too far out and the 3d distance between layers has become too small a percentage of the camera distance for the floating point math. You get the same effect from 3d layers being too close together in Z with a normal camera (for instance 0.1 units is not usually enough to get correct layer ordering).
Its not a true fix but you could put an adjustment layer on top of each 3D layer and that would flatten each layer out so they are all seen as 2D after their 3D calcs have happened.
Try bringing the camera closer (ignore any distortions for now just to find the problem) and see if the reordering issue goes away.