There is no code in Openshot that we can change to fix this, the problem
is with either MLT or ffmpeg. You could try logging a bug with MLT,
here:

http://sourceforge.net/tracker/?atid=613414&group_id=96039&func=browse

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Bugs, which is subscribed to OpenShot Video Editor.
https://bugs.launchpad.net/bugs/857761

Title:
  Loosing audio sync when editing mjpg material

Status in OpenShot Video Editor:
  Expired

Bug description:
  I use movie files from my stills camera, that are motion-jpg in .avi 
container, 640x480@30fps. Embedded audio is uncompressed 8 bit PCM (mono) 
sampled at 11024 Hz.
  If I put a clip on the timeline, cut it in two and place the last part first, 
then the audio looses sync in the part that is moved from the end to the 
beginning. 

  Linux Mint 11.04 and earlier versions
  OpenShot 1.4 and earlier versions from PPA

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