When customers reply to ticket emails, the comments are appended correctly and working fine.
When an agent replies to notifications, the comment is appended to the ticket with none of the email text and a message "WARNING - EXTERNAL SENDER". I played with this quite a bit and discovered that if I changed the TO address on the email reply (notification emails come from jira@mydomain.atlassian.net) to our standard ticket email (helpdesk@mydomain) the comment appended correctly as desired.
Is there someway i can change the default reply-to on the notifications email? or is there something I missed setting up on the mail handler? I see that i can change the sending address for the project notifications, and presumably that would solve the problem, but i'd like to see if there is another way without doing that.