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Could you confirm number of events, number of alerts and number of emails. Graham Parker in the original post mentioned 1 event to 3 SCOM alerts in the SCOM console but no details about number of emails.
You seem to have a different issue 1 event to 1 SCOM alert in the SCOM console to 3 emails. Do you include the workflowid and subscription id in the email to confirm that they are all from the same workflow \ subscription?
Does this only impact rules? Or rules and monitors? If monitors then I'd suspect a misconfigured monitor that is triggering health state changes so that it looks like you have only one alert but if you look at health explorer you'll see the monitor doing a quick flip \ flop similar to what Kevin explains here - https://kevinholman.com/2009/11/24/writing-monitors-to-target-logical-or-physical-disks/ (I appreciate you are not doing disk monitoring but the concept is the same).
Perhaps create a closed alert view on that specific type of alert and confirm that an alert isn't closing straight away. Do you have any automation tool that manipulates the alerts that might be impacting this?
You have also mentioned forwarded events. So to confirm; you have configured Windows Event Log Forwarding so events are being forwarded from the event log on one server (which I'm guessing does not have a SCOM agent installed) to the event log on another which does have a SCOM agent installed. This isn't something I've done in the past but I might be able to test in my lab. Which log is this ? Security? Is it from Domain Controllers? Password reset events?