Hi,
We're having a similar issue where some (not all) emails where they're replies to the Jira Emailed notification, are creating new tickets rather than linking to the issue as a comment.
However I don't believe that your permission answer applies here, as I was able to replicate it with my account and I definitely have permission as one of the administrators of the Service Management Project.
For elaboration, Client Raised a ticket > Team fixed the issue and closed the ticket > Client replied to me specifically (not service desk) > I readded the service desk email and replied to him. This then created a new issue, rather than add the comment, however the issue key was always present in the subject line.
Is there more details/requirements you can provide on exactly what the system uses/looks for when matching emails to issues.
Thanks
Andrew