Hi! I'm pulling my hair out over this issue. I'm attempting to create an animation that uses an isometric perspective. I followed some various tutorials to set this up, and they all behave in generally the same way. You set up a camera, position it very far out in the Z axis, and then zoom back in by the same amount, removing any perspective warping the camera might have given and essentially showing you a flat projection. You then parent the camera to a null and rotate the null using some specific angles to get the correct isometric perspective.
I've set up my cube in this composition. The problem comes when rotating the cube: the layer order seems to take over, so when the cube is rotated some layers intersect one another. If I reorder the layers so the "correct" layer is on top, this issue is corrected. But then when I rotate the cube the other way, it has the same issue. Here is a short clip of what I am talking about: https://media.giphy.com/media/lrsdiyr1YIZlbOlsEW/giphy.gif
I've tried several variations of having the "sides" of my cube be continuously rasterized, the layers inside each being 3d layers or not, or continuously rasterized or not. I got it to work with one configuration which was: All layers in the "Sides" precomps were both 3D and continuously rasterized, but the top-most "side" compositions were not continuously rasterized. This made it so the layers behaved in 3D as expected (I.E. you couldn't see through the layers) but when scaling up and down things became blurry which can't happen as I need to scale this cube up and down in my animation. Here is a clip of the intended effect: https://giphy.com/gifs/f3qB4hpZhmw8gS3Ozb
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.