My SO, who happens to be an English studies major, has ruled that your use of the past perfect tense in "Jira had failed to start, but we're back up and running again" is without justification, and that you're better off using present perfect ("JIRA has failed to start up") or past simple ("JIRA failed to start up").
Those two phrases lose information that the current one gives us, and both could, and would, be wrong.
It tells us that Jira had failed to start, but has now been restarted.
I agree that it's slightly clunky, but the current message is correct, whereas the others are not, depending on interpretation.
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