I am having the same problem relinking AIFF 48KHz 16-bit files from one FCP system to the other. They are the same exact files, but are off by 4-15 frames in length so the length and end time code attributes don’t match.
I noticed that the original system is running 7.02 while the system I tried relinking them on is running 7.03.
Not sure what versions you are using or used since it was a while ago that you posted.
I am going to try and update the 7.02 version I am using at work an reimport the audio files to see if it makes a difference.