AME: Audio "restarts" when encoding to MP4

I have several long video clips (like 60 to 90 minutes) that I'm converting from MTS to MP4. On some of them, somewhere in the middle of the video stream, the audio stream restarts from the beginning of the file. In other words the audio goes out of sync and restarts from the beginning in the middle of the video file. This occurs in AME. It appears work properly when encoded inside PP.