What version of Notes are you working with? Under 6.5 if I go under User Preferences... Mail... I show a checkbox labelled "Show a popup" under When New Mail Arrives. Are you on 7, or a version older than 6.0? Also, what platform?
Keep in mind you can activate the Notes Minder utility for the user (should be under the Lotus Applications group under the All Programs list, or thereabouts), and set it to run at startup. Notes doesn't even need to be open then, and the user can have a popup notification that is seperate from the main app. It just runs in your System Tray, and I've had better luck with it than with the feature built-in to Notes.
Also bear in mind -- the way Notes polls for new mail is poorly-designed (compares numbers locally from an .INI to a number stored serverside), and in many cases a user will have checked and read any new mail before the Domino server gets around to even notifying them of it. So even with all sorts of notifications setup it won't always work right 100% of the time.
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