This is an old post, so I’m not sure if you’re still interested in the answer, but I’ve been dealing with similar problems and have read that other people have had problem with drop shadows in Motion also. In my project, they caused the associated images to oscillate, jumping around and warping in size–especially when I tried to include a video file in the layers.
My work-around was to manually create the drop shadows with a blurred shape layer. But you could always do it in Photoshop or Illustrator, or Gimp if you don’t have those.
Even if this doesn’t help you out, hopefully it will save someone else from wasting the time I did trying to figure this one out.