Thanks for the information on the steps to troubleshoot the missing emails. If you have not considered opening a Support ticket you may want to review the following two folders to see if there are any indication of the emails either being removed or possible placed into another location.
From what we have observed in the past is that either Declude was intercepting or removing the emails prior to delivery and in some instances the PROC folder in SmarterMail held the emails inadvertently.
As Erick mentioned, do you have any specific email scanning software or possible third party virus applications such as Declude installed ? The other possible issue could be the PROC folder contains the emails. We have observed users enabling this security option in the SmarterMail application and not realize that this process will place messages into this folder to be analyzed in the background.
Security Shield | Antispam administration | Options | Enable spool proc folder
While the messages are in the Spool Proc folder, .hdr can manipulate elements of the message, such as edit, write, and add headers. Once the scan has been completed, the message will be placed back into the spool.
If I recall, the default location to the Declude log folder is: [C:\SmarterMail\Declude\logs.] and the default location to the Proc folder is: