Audio tracks lost

[georgedorn]

I have a source video in an Matroska container. There are three audio tracks; the first was captured by OBS, and the second two have been around a bit first, through an audio editor for compression and EQ and conversion to high-quality VBR mp3 before being added back to the container.

Here's my command:

auto-editor 2024-12-2019-36-30_1.mkv --edit audio:threshold=0.1,stream=1,mincut=1s --margin 0.5s,0.5s --silent-speed 4 --video-speed 1 --keep-tracks-separate -o speed4_experiment_0.5s.2024-12-2019-36-30_1.mkv --video-codec h264

The resulting video file contains three audio tracks, but the last two contain only silence.

Are there edge cases around certain source audio codecs, like don't use MP3 or don't use VBR or something?