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Currently, I think the dock and menu bar counters will only show the number of Due Soon and Overdue items in the database. Looks like this is the first time we've gotten a request for the dock/menu bar badge to count Flagged items.

Folks that want to see this will want to send email to the support ninjas so they can add your emails to the development database; the number of customers interested in seeing a change is one of the metrics we use when planning our work on OmniFocus. Thanks!