Note also that Motion doesn't necessarily preserve the scaling or positioning of the original PSD layers depending on the canvas size, which may be what you are encountering here if you are seeing stuff on the edge you didn't expect.
As Chris says, it's often best just to flatten the layers rather than use a PSD if that is causing headaches. (Note that only some formats preserve the transparency - e.g. PNG will but JPEG won't.)
Simon Ubsdell
http://www.tokyo-uk.com