It seems there's a bug or some sort of issue with .motn files being loaded into FCP's timeline and rendered. When un-rendered and you Option + P play them, or scrub through them they look fine. They even play in the viewer normally albeit a bit choppy.
But when you render them in FCP they appear as completely black.
There are a few threads about this at Apple here and here and here.
The solutions offered there didn't work for me so I'm thinking it may be a video card/driver issue, some obscure setting or incompatibility between settings or just a bug.
The workaround is to export a rendered clip from Motion then import that into FCP for me at least with FCP 6.0.1 and Motion 3.0.1.
One interesting thing is that this works as expected when using one of the new glass screen iMacs and FC Studio 2 so maybe it's a video card incompatibility or a limitation of some video cards.