I have at least one internal agent who reports that a customer can reply to a ticket, and it can take up to an hour for the agent to receive an email alerting them to the addition. However, other changes such as closing a ticket result in a very quick email.
This of course slows everything down as the agent doesn't know that the customer has replied.
I would highly recommend reporting this to Atlassian support so that they can login and take a look. It is very difficult for the community to support this type of performance issue. With that said I would ask the following:
Are you using the native email handler or possibly an add-on email handler?
Are you experiencing this behavior across multiple projects?
Are you experiencing this behavior with different customers and customer domains?
Sharing those answers with Atlassian support would expedite resolution I think.
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