The issue is most likely because you are editing with H264 , which is a delivery codec. You should be converting the clips to Pro res before bringing them into FCP and then exporting with current settings. You can then use Compressor to convert your footage to H264 or what ever your delivery codec will be.
I know you said you've done it this way before but eventually you will have problems like this.
Thanks. Yeah, since I never had the problem before, I was thrown off. Someone over at creative cow mentioned converting to Pro Res so I did it earlier tonight. Worked like a dream. Edit renders out perfectly now. In the future, I'm just going to have to take the time to convert before editing.