JIRA appears to be having trouble deleting e-mails after they're imported as issues so we're seeing many duplicate issues.
Most of the time, messages are deleted succesffully, but a few times a day one gets hung up and JIRA goes on an issue generating rampage until someone alerts us so we can go in and delete the message.
Any recommendations on a solution?
I'm afraid that's mostly up to your mail server. Jira will be trying to delete the email, but if it fails, it can't really have any way to deal with whatever the cause of the failed deletion is, so it just picks up the mail again, and repeats the process.
The short answer here is that you need to debug the mail server to find out why it's breaking and not letting Jira delete the mail after it's processed.
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