When a user sends emails into maileater, it appears that only some of them are being processed. Not all of the emails are generating Service Desk tickets.
It may be that the maileater process of a Development or Test instance of Service Desk is configured to check the same mailbox as the maileater process of the Production instance. In that case, the Test or Development instance may sometimes pick up and process emails from the mailbox before the Production instance's maileater process performs its next check of that same mailbox. Emails that are picked up by the Development or Test instances of Service Desk are the emails for which tickets are not generated in the Production Service Desk instance.
Check the options manager of any Development or Test instances of Service Desk to make sure that the maileater options are configured for a mailbox other than the one that is being used by the Production instance.
If you find that a Development or Test instance is using the same mailbox, edit the options for the mailbox name and password, specify a different mailbox, save the options, and then recycle services on that instance. The Production instance should then be the only instance checking the mailbox to which users are sending their emails.