Then I use an over node to put the foreground 3D movie on top of the backdrop. The backdrop moves and changes perspective but it slides around a bit under the 3D movie. After a lot of messing around with my camera data, I try making the backdrop the same size as the 3D movie and the tracking works fine - the 3D elements in the rendered movie align with the background.
Now this is not a huge problem because even for bigger backdrops, all I do is use a viewport node and the tracking works without cropping out the image or downsizing. However I'm still wondering why this is the case because on p497 of the Shake 4.1 manual, it shows a bunch of images connected to MultiPlane nodes and they don't look the same size nor do they need viewport nodes. I don't understand how the image size would affect the tracking anyway.
I don't think it's a MultiPlane setting because in the manual they have different sized inputs going into the same node.
On a side note, does anyone know how to stop the transform handles in the viewer from scaling? When an object gets really large or small, the rotate handles practically take up the entire viewer or almost disappear, which is ridiculous. There has to be a way to keep them at a fixed size. The handles should stay at about 50% of the size of the viewer window at all times IMO.