Although I have my account configured to be sent plaintext email notifications -- which I do properly receive for one project on our Jira -- all of my notifications for another project are always in HTML format. I cannot seem to find any per-project setting. Any ideas?
There are no per project settings for email. Do you have a mailinglist create as a user in JIRA and the mails being sent out to that mailing list (which includes u ofcourse)?
You can check the 'To' field in the received mails and confirm whether both the emails are actually addressed to you.
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