If you do not have enough layers of transparancy set up, you will end up with black I think.
Try rendering one single element with the surface. If you see transparancy there, the surface settings are ok.
In cinerender go in to 'detailed settings', scroll all the way down to options > general options. Check the settings at Ray Depth and Reflection Depth, you'd really want them to be at something like 12 or more depening on the amount of layers of transparancy there are in your view. It takes 3 'bounces' of the rays to get through a plate of glass (2 layers) and show what is behind it. Flat alpha channel textures probably count as 1 layer. So let's say you have a window (2 layers) and some alphachannel texture sitting behind that window, you'd need to have at least a depth of 4. However, quite often things overlap, so I find 12 to be a nice safe number that still gives reasonably fast render times and doesn't mean I need to remember to change the settings when the model changes.
Erwin Edel, Project Lead, Leloup Architecten
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