No, that is something else. The previous post means that when you are in the Unread folder and you read a message, it is not automatically cleared away. What @NJRonbo is asking about is when he is in All Inboxes, the messages are not automatically cleared from Unread.
@NJRonbo’s issue may be so low level database corruption. He can try closing eM Client and opening a Windows Command Prompt. Not a powershell, but a command prompt.