Oh, I see you are right it is related after all. In case you didn’t know, when merging messages you can copy the topic ID number from the URL of the message you want to merge into, into the “Existing Message” field. Can you try that and see what happens?
Take a look at the email addresses in the raw tab. They should look something like this:
incoming+b249a23e7e545288e8dac00808ba154c@YOURDOMAIN
If instead you are seeing a different email address, eg the one for starting new topics by email in your category, then that is the culprit.
There’s nothing that can be done on the Discourse side to fix that - you’d have to take it up with the people you are communicating with or just live with it and move the replies manually as I suggest above if you want to keep them together.