So if I just copy-paste images, and export the file in a container, with audio and video set to copy, how is the video stream generated?
Why should encoding the video using Still Picture and stillimage yield different behaviours in the audio result when audio is still set to copy? Funny that you say it isn't a question of faith without giving reasoning for your troubleshooting methods... This is a bug, whether the solution works or not isn't really an issue, the bug exists and should not exist.
The screen capture displays both the video import glitch, and audio glitch I had mentioned. It shows that the audio glitch is only present in the export, and that the video bug only occurs on import of the finalized video.
The external audio sample would be useless, since there is nothing wrong with the audio that is imported into avidemux, just the export is bugged, which is included in the screencap. Additionally, the video bug is in the screencap so it was necessary to demonstrate both within a single simple video.
Interestingly, trying to extract the audio track from the bugged export using Audacity yields an enormous amount of silent sections which aren't present during video playback.
When you say not to use the "release", do you mean the 2.7 branch? I thought the releases linked on Avidemux were supposed to be stable branches, are you saying the nightly builds have fewer bugs than the stable 2.6.7 or 2.7 release builds?
I could try re-doing it on one of those to see if the bug is fixed before trying workarounds, is there one of these you recommend?
http://avidemux.org/nightly/win64/