It seems when a new ticket is open by the web interface, after it has been closed (eg reply and close), if the user replies again by email to that now closed ticket it then opens it as a new ticket and does not re-open the same ticket, even though it has the original ticket number in the subject... which ends up being confusing because the subject now has two ticket numbers in it. This does not seem to be a problem when a ticket is originally created by an email and not the web interface.