We’re running at this commit: new 'private_email_time_window_seconds' site setting · discourse/discourse@2d17071 · GitHub
I guess I’m not clear where you’re asking to look … If I filter /logs for “mail” I only see a couple errors about creating incoming email posts.
Unfortunately Mandrill logs don’t seem to show the reply-to key. I can confirm that even this morning one of the users with the issue got 2 otherwise-identical reply notification emails, processed by Mandrill during the same minute. Can’t confirm the reply key unless there’s somewhere else I could look.