Some notifications aren't really about any page. Currently, those notifications are not associated with any page, and so they won't be displayed if you filter by a page using the (future) sidebar on Special:Notifications, no matter which page you filter by. This also means the number of notifications for each page does not add up to the total number of notifications for that wiki (although that can already happen when there are many pages, because we don't show more than 10).
The solution will be to add the following notifications (currently page-less) to the user's page:
- thank-you-edit (once it stops defying the laws of nature and we turn it back on)
- unsubscribe-bouncehandler (sent when we stopped sending you emails because they bounced too often)
- gather-hide (but Gather's been undeployed, so we don't care)
- EducationProgram-related notifications about you having been added to a course in a certain role (only in rare cases, probably a bug)
- These all seem reasonably user-related, so I think putting them in the "user" group is OK.