Comment 2 for bug 856642

It's not meant to show unread messages - but new messages - as per the spec: https://wiki.ubuntu.com/MessagingMenu#Recommended_behavior_for_e-mail_clients

"For the purpose of the messaging menu, a new message is an unread message that the program discovered since the last time you (a) performed any action in that mailbox or (b) selected the corresponding item in the messaging menu."

So, navigating to a folder will mean that folder has no new messages anymore, and this is independent of unread messages.