David,
Assuming you are viewing this stuff on a good monitorn not your FCP windows, you should check all your settings, quality settings and make sure you do a final render. When you go to make a DVD, if you go directly from your FCP timeline to Compressor, all your graphics, effects and transitions will be sent directly to your mpeg file, bypassing DV compression. The resulting DVD is noticeably better than one made from a QT movie, plus it will automatically have compression markers so your motion footage will be smooth as silk.
I incorporate Animation movies from AE all the time, and they always look perfect.