I recently lost 2 days on this very same problem. I was exporting a HDV sequence (46min duration) from FCP, 1080 60i compression with 48k audio – I exported about 2 weeks ago and it worked fine, then it all went crazy – all I changed was a cut.
So anyways, my fix came from another forum – try copying all the tracks (audio + video) from your sequence into a new sequence and paste it in. Then export from this new sequence. When I pasted all my stuff into the new sequence it all required rendering so I ignored that and just exported. The result was fixed, fully sync’d video.
Hope you, or anyone else looking for answers, find a help in this.
Regards.
Simon.