We get a lot of calls about missing mail in the Inbox. The Inbox icons shows a new unread mail, but this mail is not visible at all.
You reply on a mail from with a folder and the recipient is also replying on your mail back to you. The Inbox folder shows us 1 unread mail indication. But when you open the Inbox, you don't see any new mail. When you disable the MailThread Group option, you see the missing mail. Or when you open the corresponding folder, you can see the mail inside the mailthread.
The Inbox situation is very confusing because the Notes Client and iNotes are different in show mails in threads. In these client you see the mail inside the Inbox.
Please rethink the MailThread design in order to get it clear where and when you see the unread indicator and/or maillocation when you receive a replied mail from a mail inside a folder.