If you have old unread notifications and more than 25 read notifications, it is possible for the badge to show a positive number but the flyout/popup doesn't include any unread notifications.
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Change 297614 had a related patch set uploaded (by Sbisson):
Sort bundled notifications by read status AND timestamp
I'm hoping this to be fixed and released today. I don't know if it has affected anybody yet.
Change 297614 merged by jenkins-bot:
Sort bundled notifications by read status AND timestamp
Change 297855 had a related patch set uploaded (by Mattflaschen):
Sort bundled notifications by read status AND timestamp
Change 297855 merged by jenkins-bot:
Sort bundled notifications by read status AND timestamp
Checked in betalabs - the notifications are sorted by their status and their timestamp. e.g. If #of notiifcations(read and unread) >25, unread notifications will be displayed on top of the list. If # of unread notifications >25, as soon as you click 'mark all as read', the unread notifications from the "next pages" will be displayed at the top.