Hello Anthony,
This appears to be a side effect of how IE handles focus. When an event like a message being marked as read happens we ensure that the mail list is refocused so hotkeys continue to work on it. IE though apparently allows other windows to also take focus away from each other so when the main window focuses the list it pushes the popout behind it. Modern browsers (including Edge and Safari) don't allow this as it clearly can be inconvenient to users, but unfortunately there isn't a simple way around it for IE.
Regards,