Hi Steven,
Unfortunately we need an example FCPXML with a clip that demonstrates the issue to progress. As you have the same problem if you can provide the FCPXML a picture of where you see the discrepancy and the audio file where the issue is seen, we would be happy to investigate and resolve.
Happy to send you details of an ftp site to upload the FCPXML and audio file, and or sign any NDA you may require.
Many thanks.
James.