If you're using Motion 1.0.1 with Mac OS X 10.4 Tiger and apply a Compound Blur without a blur map to a clip, the effect can make the clip transparent.
To prevent this issue, add an image or movie to the Blur Map well in Motion, in either the Inspector or the Dashboard.
The Compound Blur filter blurs an object using a specified channel of a blur map image. You can use a shape, still image, or movie file as a blur map image, and select any—or all—of its red, green, blue, alpha, or luminance channels to dictate the overall shape of the blur.