We have had one other report of this as well, however through our analysis we determined the items were missing due to a massive POP deletion.
However, since you don't see any POP3 traffic I would highly urge you to open a support ticket with us so that we may investigate further to see if we can track this down for you.
We do have some mailbox logging that can be enabled that will log deletes, new messages, etc into a debug log file that you can analyze to see if you can find the source of the deletes. This can be enabled by editing the mailconfig.xml file located by default under C:\Program Files (x86)\SmarterTools\SmarterMail\Service. Within the logging section you'll want to add the following under the logging section:
Once this change has been made, you'll want to stop\start the SmarterMail service and once the issue surfaces, you should find a mailbox log for these users under under C:\SmarterMail\Logs by default. If you cannot locate the source of the deletes within this log file, please open a ticket with us and we can analyze the log further.
Technical Support Supervisor