I saw the area below on the forums I’m just not sure where to put the changes. Is this in the gui somewhere?
If you’re using a FFMPEG profile, trying setting the -ss parameter to -ss 30 to see if that solves the problem.
Try setting the <encoder>-audiodelay=skip for the profile you’re using.
If point 2 does not work, then you can use the same parameter and replace skip with a +ve or a -ve number. This will advance or retard the audio by that many seconds. This can help bring the Audio back into sync with the Video through trial and error. Make sure you replace <encoder> with the profile encoder you’re using. e.g. ffmpeg-audiodelay=1.25
If you’re using MEncoder in your profile and your audio is going out of sync ONLY when commercial removal is enabled then try to use the mencoderedlskip=true option to use the MP4Box fallback method to strip out commercials. (again this will only help if commercials removal is causing the desync in audio while using MEncoder).
If you’re using FFMPEG or Handbrake and .mp4 or .m4v outputs then try playing with CutMP4Alternative=true
Try setting UniversalCommercialRemover=true if the above doesn’t work.