I have a basic video in Final Cut that uses an alpha channel that I'd like to bring into Motion. I export using Quicktime conversion, Animation codec with "Millions+". I then bring in the clip into motion, but am left with all "alpha" areas filled in with black. I attempted to manually adjust the Media settings in case Motion was improperly "guessing" the alpha channel, however this provided no solution. This is a method I could have sworn I've used successfully in the past, but now I'm getting no results.
I'm able to achieve a similar effect by laying down a green matte under the video in Final Cut and then applying a "Color Key" and "Desaturate" filter combo in Motion, but the jagged edges this produces leaves much to be desired.
This is usually caused by FCP's insistence on assuming you don't know what you want.
Umm, sorry, I'll restate that:
FCP is probably exporting the rendered clip, not the original clip. If your working sequence settings are DV, there is no alpha channel.
Try unrendering the clip (control-click> remove attributes) and export it again using Animation.
This is my standard sigfile so do not take it personally: "For crying out loud, read the freakin' manual."