The Email listener may ignore emails sent to the Inbox unless the Inbox Configuration option "Ignore Cc BCC Emails" is checked.
The issue where emails are ignored, can occur where the Inbox email address gets replaced by the Email Server.
The user sends an email to the email address 'firstname.lastname@example.org' but the email listener receives the "To:" address from the email server as something different: '<servicedesk>'.
Since the Inbox address 'email@example.com' was replaced by "<servicedesk>", the Email Service verifies the "To:" list, but is not able to find firstname.lastname@example.org', it considers the incoming email sent to this Inbox as a "CC/Bcc". Since the 'Ignore Cc/Bcc' flag is not checked the Email Service ignores the incoming message.
Check to see if the Email Server at is modifying the "To:" email address when the email listener downloads the email.