This issue had me pulling my hair out, but there is a fix.
Export your video out as a quicktime file without the audio (use export via quicktime conversion) from FCP.
Next Export your master mix audio as AIFF from Soundtrack Pro.
Open both of these files in Quicktime 7 (not Quicktime X).
Set an in point and out point at the beginning and end of both the audio file and the video file.
cmd+c the audio or use edit>copy then select the video file and go to edit>add to selection & scale.
This will insert the audio into the file and stretch it to match the length of the video.
Voila, the video and audio are now together in one file and in sync.
Save the movie as a self contained file and return it to FCP. Now you are free to either use this movie file, or just it’s audio.
Don’t try and export the audio from that movie as a separate AIFF because it doesn’t work.
Hope this helps
Richy