1. Mailserver : Mail>Settings>Filters>"Enable server side mail rules".
2. Web Server Web>Sites>(your https site)>Web Services>"Allow users to configure server-side mail rules". This provides an interface for users to edit their server-side rules.
Solution:
Turning the (1) "Enable server side mail rules" off (wait a minute) and on again, cleans out the buffered. I am not sure if it reloads the messages again, or if that happens overnight.

