Created attachment 78174 [details]
demonstrates bug with 2 working and 2 broken examples
A 3D transform has no effect if any ancestor element also has a 3D transform, and if the transform operates in the Z direction (translateZ, rotateX, rotateY).
The provided reduction has four examples with two cases each, one where both transforms are applied directly to the colored squares, the other where the rotateY is applied to the containing element of the same size.
The first two examples work correctly in both cases because the transforms rotate/translate in the X/Y direction.
The second two examples do not work in the case where the rotateY transform is on the containing element because they rotate/translate in the Z direction.
This is working as expected. You need to set transform-style if you want the elements to share a 3D space. See example at http://webkit.org/blog-files/3d-transforms/transform-style.html