OK, things to try.
1. The Email Manager only logs jobs that are marked as unread. Typically, these are bold. Are the emails marked as unread?
2. Double check the Email Manager Profile filters. Is a filter criteria cancelling out these emails? Are you filtering by subject, message body or both, or none at all?
3. Is the profile that you are using to target these emails enabled? Is there such a profile?
4. If the email are being delivered to a specific email folder, does the network account that you're using for the Email Manager service have security permissions to read, and modify this email account? This would be an Exchange / Outlook setting.
5. Try turning on the "Verbose Logging" option in the Email Manager service setup screen. This will provide more diagnostic logging information that might isolate what's going on.
6. Check the Windows Event viewer for the Email Manager. Although the Email Manager creates its' own log in the HelpMaster database, it also writes to the Windows Event log, and sometimes this will reveal a message that for whatever reason does not make it to the database log.
7. Is the email sent by Sharepoint generated by code, and if so, is it malformed perhaps? Sometimes if you're manually coding an email, if you mess up the coding of the header, sent address etc, it may look good, but underneath, it's corrupt.
8. Do you have a global filter / block on the any email addresses or domains - Check the Email Manager Profiles, global options tab.
9. You could try running the Email Manager with a different (higher privileged) service account. If it works this time, then it's a permissions issue. Try the domain admin for starters.
Hope these help troubleshoot this issue.
Best regards
Rod