When I "mark all as read" in my notifications, it seems to work, then when I go back, they are all "unread" again. This wastes my time clicking to see new posts, when there aren't any, which is annoying.

A developer friend said this is a ploy some sites use to get more clicks to get a higher ranking on search engines. I hope that's not what you're doing, because if so, it's pretty underhanded. Hopefully, it's just a glitch that you will fix soon.