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So it appears it was an internal issue with AWS MediaConvert. They fixed it really quickly after confirming the issue.
answered a year ago
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I have also noticed some weirdness with MediaConvert recently. I'm not sure if it's related or not. We have been clipping some videos to extract a portion of the video from the middle. When we specify a start time/end time, AWS seems to be choosing values that are a few seconds off instead, and we haven't been able to figure out why yet. I can't yet say for sure this didn't happen previously, but user bug reports have been in the last week or two. ffmpeg seems to reproduce the same behavior when avoid_negative_ts is not set to make zero, which also may affect audio/video syncing.