Follow up: I appear to have solved this and have some further
information which may be useful.
TL;DR: Setting AVStream's avg_frame_rate, which corresponds to mkvinfo's
"Default duration" field, appears to have fixed this.
From my investigation, it appears VLC will use a few different sources
MattKC:
> ==Summary==
>
> I've been implementing ffmpeg/libav into an application, and have run
> into timing-related issues when playing back Matroska/MKV videos created
> by my application in VLC. I tried asking about this on the libav-user
> mailing list and received no response so I thought I'
