The administration in-box is associated with comments made relative to a report / dashboard / storyboard that that specific
user has 'subscribed' to. If another user comments on that report, that you've subscribed to, you will receive an alert in your in box.
For general discussions, these are all contained within the 'discussion' tab and it's expected behavior that users will be checking their timeline for updates on these types of discussions. Unfortunately, there is presently no feature that would tie a general discussion comment to show up as an alert in the admin in-box.