audio inconsistency when exported to .mov

[Former user]

Trouble with muxing audio from a 5d mark 3 exporting longer sequences of .MLV files. When previewing .mlv files it always creates a full wav audio file which contains the full audio. However when hitting export "E" converting to .mov, the then created wav file for muxing often is shorter missing a big portion of the audio. I had longer .mlv files (containing 3 files or more) that have half the clip muted. So, wav created in preview are fine. Wav created for export to .mov often shorter.

I,m on a macbook pro retina 15 inch, nvidia 750m graphic card. 5d mark 3.