The Zen Cart software sitting on your server always sends emails immediately. It never delays the emails.
Since Zen Cart runs on your own server, all delays in sending of emails are related to your own server's email processing.
If it is sending new messages about an order "later", then it could be from:
a) something gone wrong on the hosting company's email infrastructure. They would have to answer to that.
b) someone in your Admin is updating statuses on those orders, and that's triggering an update email to those customers. These would NOT be "duplicates", but rather would be status-updates
c) maybe your server/site has been hacked and an intruder is in there doing inappropriate things.
Ref http://www.zen-cart.com/wiki/index.php/Recovering_From_Hacks
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