I get this inside After Effects
when i render i get this
The intersection betwhen layers can be seen but not the shadows.
Here is the project file.
Your comp preview is set to 25% and a custom resolution. This cannot work 'cos inevitably adjusting effects on a reduced resolution preview will look different than at 100%. Serously. You need to check your settings at full res. That's all therte is.
When you give us a screenshot it's useless to just show the comp window without revealing the properties (press the U key twice) of the layer in question. It's also not necessary to scale down the screenshot to 400 pixels wide. When we click on it, we can't see anything. Your first screenshot, linked through DropBox doesn't show what effects you used.
I pulled down your project and you used a 3rd party plug-in VC Reflect. That information would have been helpful.
I don't have the plug-in installed on this machine so I can't tell what may be wrong, but I suspect that if you follow Mylenium's advice you'll see what you expect to see.
I'm not sure what you are gaining by making your pre-comps 3D. Your composition layout is a bit confusing to me. Maybe it would make more sense if I installed the plug-in