I'd thought that perhaps this was because we were rendering the PNG and then writing it to a file via PHP, so I made https://github.com/wikimedia/svgtranslate/pull/99 that uses shell-level redirection to do the same thing. Doesn't fix the problem though (still, it does feel a bit faster in my testing, so maybe it's worth doing anyway).
I've also turned off response buffering (on the staging site), and that seems to maybe have helped. Unfortunately, all the example images above are now working correctly so I'm not sure.
Will keep investigating.
I'm not currently able to find another example of this issue. Maybe the culprit was the Nginx proxy after all. If anyone finds another broken image please send this back to the in-development column.