Turning ON either one or both of the following functions in RAW Video (MLV) causes out of sync audio recording: Use SRM Job Memory, Extra Hacks.
Noticed that the "out of sync" can be split up to 3 sections. A 20 seconds long MLV file can have audio from original 18-20 seconds playing in the beginning of the clip, then 12-17 seconds of the original, and finally the original beginning of the audio track plays til the end. The issue is apparent when playing files in MlRawViewer_1_3_3. A 27 seconds long clip in MLV (825MB) conveying the issue can be downloaded from here: https://drive.google.com/file/d/0BzDJkyUbS4xgZnRnbjFTeERzUk0/view?usp=sharing