Whenever I click "Mark all read" in the Update Notifications section, I actually have to do it two times to get it done. The first click pops up a message saying that they've all been marked as read but they haven't. The second click will pop up the same exact message but this time it actually marks them all as read & clears out the notifications.
I'd attach a screenshot for you but all my Project Subscriptions have disappeared with my email address change. I'll try to monitor & get you a screenshot once that's resolved & I have new notifications!