Here's a capx where I'm experiencing this trouble. It seems like anything below the layer "main" hides behind the layout.
https://docs.google.com/open?id=0B70_mwq_gjY7Sm5CaVVRSDlyZms
You have transparent set to No on the 'main' layer.
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Haha, thank you. I didn't even know that was a thing. Saw somebody else's thread but no bug reports about it, so I assumed it was a bug. Thanks :)