Using blending modes with 3D layers is a very different experience. There are SEVERAL new rules to keep in mind when you promote a layer to 3D.
Use 3D Comp Views to determine actual order in Z-space. The order in the Timeline window does not change.
When using the Standard 3D rendering plug-in, only those layers behind will be affected by the blending mode
When using the Advanced 3D rendering plug-in, the mode is applied pixel-by-pixel. In other words intersection is taken into account. This produces more accurate blending.
Layer Order in the Timeline window still affects track mattes. The layers must still be adjacent, however this may lead to unexpected results. Consider pre- composing the two layers (but don't collapse).