First of all, what AWS version are you running?
The alerts can't be active or inactive. If it's an alert, in the log, you see "Alert" and when the cron job deletes them, they are gone. Also, the kill_alerts.php script, when run, should leave a log with the names of the users for which the alerts it removed.
Check your kill_alerts.php, if it is different than the one in the latest version, please upload the latest one.
Rgds
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