It could be a couple of things:
1) The codec of your FCP sequence. For instance, if your sequence is DV, then you are rendering your Motion project into DV, which is destroying your motion graphics.
2) You are judging the results by FCP's Canvas, which does not show you what your final output looks like. For more info, you could check out this article:
[
daystreet.com]
3) The combination of both 1) and 2).