So many things that can go wrong, so little time ....

I can't really say. If I could see your material and render settings, I might have a better chance of identifying the problem. It might be as simple as failing to enable "render over background shader" in your render options, or neglecting to set Quality to "current render settings" in your Make Movie options.

You do have Service Release 3 installed, right?

You'll definitely want to save your current scene and start over, experimenting with a blank scene (preferably in draft mode, at low resolution) until you get the hang of animated materials. Do a few still-frame test renders at different points on the timeline to make sure everything's rendering properly before you commit to a full-sized, full-length render in production mode.