Notifications to watchers are not being sent when a new comment is added through an issue

Summary

When replying to a notification of a specific JIRA issue with Microsoft Outlook or adding a comment through email, a comment is added to the issue, but no notifications are sent to the watchers when the notification scheme is configured properly.

Steps to Reproduce

With Outlook

1. Create a mail handler to a specific project
2. In Issue Commented (Notification Scheme), add a notification to All Watchers
3. Create an issue
4. Ensure to set a few users as watchers
5. Send an email out to JIRA's mail handler with the issue key of the step 3
6. A comment is added to the issue
7. No notifications are sent
8. The log files (atlassian-jira-outgoing) show noting even with debug

Expected Behavior

The watchers should receive the notifications properly 

Workaround

Use the web client