I've put a permanent fix for this in the next mcebuddy build. Also updated avidemux and put some control checks for the issue.
The issue was your orignla file has a annexb requirement which avidemux could not handle and hence it messing up the video while merging it. This is now handled by falling back to ffmpeg to merge the video is this issue in encountered.
The issue was your orignla file has a annexb requirement which avidemux could not handle and hence it messing up the video while merging it. This is now handled by falling back to ffmpeg to merge the video is this issue in encountered.