Andrew Bernard writes:
Replies to threads from that mailer keep sometimes being properly threaded in Hyperkitty and then randomly jumping out into a new thread.
I don't understand what you're describing here. Is the archive public so that we can look at it?
Yet the threading appears to be correct in mail programs such as Thunderbird,
Then it's probably a Mailman (HyperKitty) bug. #216 looks like it might be responsible, although in another message you say you think it's fixed in your instance. Again, we need more information to be sure. It's sometimes the case that for various reasons a site has multiple versions installed and the one the site thinks is running isn't actually handling the mail or the archive or whatever.
Possibly some interaction with other RFC-822 headers?
Seems unlikely. Some threading algorithms use only References, others use both References and In-Reply-To. However, in most cases In-Reply-To is just a copy of the most recent message ID in References.
To check hypotheses about a threading bug we really need to see the Message-IDs, References, and In-Reply-To from the problematic messages and the immediate replies, at least.