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I receive this question frequently enough that I should consider it an FAQ.
So "Why does Selenium not work with my Alert?" or "Why can't Selenium handle the alert in my application?"
There is an FAQ answer on the Selenium wiki that shows the Alerts API
But that typically doesn't answer the question because the person asking the question has used the alerts API.
The answer I have given, in every single instance, takes the form "The thing you think is an alert, is not an alert"