Mark,
First, what do you mean when you say, “I set the output to H.264?” Are you changing the Compressor setting of the timeline in FCP, or are you going to Quicktime conversion and choosing H.264 compression? If you’re changing your timeline Compressor, that’s wrong. Keep that at ProRes422.
Second, don’t even use Quicktime Conversion. Export a Master by going to File > Export > Quicktime Movie. Make sure you’re exporting at Current Settings and the Make Movie Self-Contained option is check marked. Then bring your Master into Compressor to create your H.264 and MPEG files. Compressor will do a better job.
Also, you didn’t explain your H.264 settings…
